When I try to create a new project from existing code, IDEA only finds my java source directory (and names it Src.iml). It doesn't find my other top level directories - web, resources, etc. Here is an example of the exact steps and the problem (below on Mac but have the same problems on Windows). In attached zip are the 4 images I'm referring to below: I have a project called "rgrid" in /Users/rick/projects From IDEA I select "create new project" "Create project from existing sources." Type in name of project "rgrid." On next field I browse to the "rgrid" directory and select it. Now notice "new_proj1.jpg" Notice an extra lib1 dir I uncheck lib1 and continue Now notice "new_proj2.jpg" lib1 is still there and only src dir showing up as included other than two lib dirs (Now, I do have a lib dir under /WEB-INF/lib and a lib in the root of my structure so that might be why both- but if so it should list them with better names.) Now I hit continue and look at the resulting new_project_final.jpg Also look at the directory structure in Finder dir_structure.jpg and notice where it put the .iml file and it named it Src.iml In order to fix this I have to go into settings and wipe out everything and point to a new root directory and then things work.