Not sure if the way you described is the best way to proceed but here you can make use of cellfun to achieve I think what you described.
A = rand(12,100);
Ac = mat2cell(A,[6,6],ones(1,100));
B = rand(101,6);
Bc = mat2cell(B(2:end,:),ones(100,1),6);
Created sample data. Ac is a 2x100 cell array with 6x1 vector in each cell. Bc is a 100x1 cell array with 1x6 vector in each cell. Now cellfun to multiply vectors in each cells
BcAc1 = cellfun(@mtimes,Bc',Ac(1,:), 'UniformOutput', false);
BcAc2 = cellfun(@mtimes,Bc',Ac(2,:), 'UniformOutput', false);
BcAc = [BcAc1; BcAc2];
whos BcAc
Best Answer