You can store them in an array, where each column represent the diagonal of each block.
(I have assumed that the 64*64 blocks are cell elements.)
%Generating random data with a similar structure
%i.e. 64x64 blocks (cell array) with 4x4 block (double array) inside
C = magic(256);
z = 4*ones(1,256/4);
C = mat2cell(C, z, z)
C = 64×64 cell array
Columns 1 through 12
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
Columns 13 through 24
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
Columns 25 through 36
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
Columns 37 through 48
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
Columns 49 through 60
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double} {4×4 double}
Columns 61 through 64
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
{4×4 double} {4×4 double} {4×4 double} {4×4 double}
out = cellfun(@diag, C, 'uni', 0);
%Using horzcat to get each diagonal as column
OUT1 = horzcat(out{:})
OUT = 4×4096
65536 64512 63488 62464 61440 60416 59392 58368 57344 56320 55296 54272 53248 52224 51200 50176 49152 48128 47104 46080 45056 44032 43008 41984 40960 39936 38912 37888 36864 35840
65279 64255 63231 62207 61183 60159 59135 58111 57087 56063 55039 54015 52991 51967 50943 49919 48895 47871 46847 45823 44799 43775 42751 41727 40703 39679 38655 37631 36607 35583
65022 63998 62974 61950 60926 59902 58878 57854 56830 55806 54782 53758 52734 51710 50686 49662 48638 47614 46590 45566 44542 43518 42494 41470 40446 39422 38398 37374 36350 35326
64765 63741 62717 61693 60669 59645 58621 57597 56573 55549 54525 53501 52477 51453 50429 49405 48381 47357 46333 45309 44285 43261 42237 41213 40189 39165 38141 37117 36093 35069
%For check, compare the diagonal of kth array to the k-column of output
%Here k is 1
C{1}
ans = 4×4
65536 2 3 65533
257 65279 65278 260
513 65023 65022 516
64768 770 771 64765
If you want to print/display them as a vector -
OUT2 = vertcat(out{:})
OUT2 = 16384×1
65536
65279
65022
64765
64512
64255
63998
63741
63488
63231