Virtual geometry assurance is a key component of today's product development. Much of the virtual geometry assurance is done in Computer Aided Tolerancing (CAT) tools. Earlier research has shown that manual assembly complexity influences the geometrical quality of the product and that assembly tolerances are seldom used in CAT simulations for manual assembly parts. In this study a method for including manual assembly complexity in variation analysis in CAT is introduced and discussed. The method has been tested and implemented in a CAT tool using a real industrial case with promising results.