If A and B are the save size then instead of the "find" function (which produces linear or subscript indices) use logic indexing for speed e.g.:
L=A==2; A(L)=[]; B(L)=[];
Reshape is not required (and is slow for large arrays). The approach above and that of Mr. Roberson only work if the empty entries of [] lead to the removal of say always n colums or n rows. In other cases you'll get an error. You could use sparse arrays and set the entries to zero instead or use NaN.
Good luck, Kevin