Are you or your firm creating the part scans yourself? If so, you might want to invest in a software package that will help you compare the scan point cloud to a .prt/.sldprt file. I've used Geomagic for reverse engineering in the past, and I thought it was a very effective way to check my work as I go along.
In other words, I don't know any automatic ways to smooth out a surface. There might be some API wizards out there who can use your point cloud with the Freeform surface command to create a custom formed surface, but that's beyond my capabilities. My only method is the tried-and-true "import the .stl file and try to build a .prt file that looks just like it" method. In that case, I hope you're good at surfacing...
SolidWorks Premium has an addin called ScanTo3D which will make a smooth NURBS surface from the data. Or, if the part is as simple as it looks, you may want to just have someone remodel it in SW.
*Checks add-in menu*
Well, I'm an idiot. I had no idea SW had that.