If you are talking about the Parametric version, you only have the import data doctor (IDD) to work with. The problem is that the STL files are facet files and really don't have a lot of usefulness.
If you can get your models in Parasolid or Step format, these behave much better. However, you still have the limitation of it being a "dumb" solid. Therefore, the IDD is the only means to do some simple fixes. PTC has a history of preserving imported data, although it has become easier in the Creo regime. I bet the flexible modeling extension would help in this case.
In Creo Elements/Pro, you dont have flexible modelling to edit dumb solids. If the model is opened correctly in part mode, save it as a prt file and use that file to do assembling. If the part did not opened correctly, right click on the import geometry in the feature tree and click edit definition. You should get some option to get into the Import data doctor (IDD). Play around with options available and try to fix the issues. But dont expect too much from IDD.