Sound like what you want to do is some sort of regression analysis on your point data to obtain the best fit "pure" geometry you desire. Search cylindrical regression, or planar regression for mathematical procedure. Then construct the "pure" geometry from the resultant equations.
I think Geomagic (now owned by 3D systems) or Polyworks might offer a more automated solution.
I ended up solving my problem using a combination of Python / VTK and Fortran with OpenMP for parallel processing. Now I can align the point clouds with respect to a main plane ( I am working with cylinder heads currently) and the XY plane and then finish the alignment in the XY plane by performing a regression analysis on the proected image of the dowel holes. There are several steps (filtering points according to density of the projected image for instance) but I am now running. If anyone has similar machined parts that they have scanned and need similar alignment prior to using in SolidWorks please let me know and for a modest fee we could try to get you going. The program I have created is not currently distributable, so you would have to get me the data and I would return it aligned to your desired geometry. I am working with files around 3e6 points but since I have written everything myself I don't think there is a limitation. I can also easily reduce the point count if you need that.
Plymouth Machine Integration, LLC