For clarity, can you edit your question to remove the three instances of the word "it"? This isn't me being a stickler--I just want to make sure I understand your question correctly, and I can interpret a few different meanings depending on what "it" refers to.
Another clarification needed: what do you mean by closest value? Do you mean rounded to some nearest value or do you mean nearest neighbor in the arrangement of the matrix?
It sounds like you'll want a two-step process. First, replace the NaN elements of B with corresponding elements of A:
A=[ 2 3 4 5 6 7 ;
2 4 nan 6 7 8;
4 nan 6 7 8 8];
B=[nan nan nan 5 6 nan;
nan nan nan 4 5 nan;
nan 6 nan nan 7 nan];
% Replace NaNs in B with corresponding values of A:
B(isnan(B)) = A(isnan(B))
B =
2 3 4 5 6 7
2 4 NaN 4 5 8
4 6 6 7 7 8
There's still one remaining NaN. One way to replace it is with John D'Errico's inpaint_nans function:
% inpaint remaining NaNs:
B = inpaint_nans(B)
B =
2.0000 3.0000 4.0000 5.0000 6.0000 7.0000
2.0000 4.0000 4.2222 4.0000 5.0000 8.0000
4.0000 6.0000 6.0000 7.0000 7.0000 8.0000
