I would say that it depends om what you want to base the imperfections on. But since you say Femap let's do in in Femap.
Try with "Custom Tools" - "Postprocessing" - "Node moves by deform (with options)". Than you can move the nodes based on the deformations in a Output Set.
Another way is to do it in the solver (depending on the solver). Run the analysis and let the deformed geometry be the base for the continued analysis.
But the first option involves only Femap. Obviously you can also move the nodes individually by simple node editing but that is often impractical.