Are you saying your .stl file is only a surface model and you need it to be a solid model?
Are you saying you want your .stl file to be a working model with features?
STL files are tesselated (or triangulated) models that are generally used to send data to 3d printers. Generally you could use the .stl to reverse engineer to a working 3D model but I don't know of a way to "convert" a tesselated model in to a smooth model.
Steve Williams Pro/E Version 15/16 (Circa 1995/1996)