The aligned ranks approach indicated by Jos Feys is probably the best approach.
Abolfazl Ghoodjani , the following is a quote from a GraphPad site. This would suggest that GraphPad Prism does not conduct a two-way nonparametric anova. Do you have information that contradicts this?
Two-way ANOVA assumes that your replicates are sampled from Gaussian distributions. ... If you really don't think your data are sampled from a Gaussian distribution ... , you should consider performing nonparametric two-way ANOVA. Prism does not offer this test.