If I understand your question correctly it can be done like this: You can rearrange the dimenstions of B after the loops with commands like reshape for instance. But all your values will be stored. A doesn't have to be within the k-loop as it isn't altered there.
for i=1:64
for j=1:630
A(i,j)='do somthing over (i,j)'
for k=1:8
B(i,j,k)='do something with A (i,j) over (k)
end
end
end
B2=reshape(B,[size(B,1),size(B,2)*size(B,3)]) % or any other variation you like
