You could use cellfun like this:
>> F = @(m,x) m(setdiff(1:size(m,1),x),:);
>> C = cellfun(F,A,B,'uni',0);
>> C{:}
ans =
4 5
ans =
1 2 3
1 4 5
ans =
3 4 5 6
8 9 0 8
3 4 5 6
or use a simple for loop:
>> for k = 1:numel(A), A{k}(B{k},:) = []; end
>> A{:}
ans =
4 5
ans =
1 2 3
1 4 5
ans =
3 4 5 6
8 9 0 8
3 4 5 6