Hi nick.prsha,
To remove the extra solid bodies in the part you can use the Delete Face tool > Select Lump button as shown.
3D Model tab 
Modify panel Delete Face 
Also, depending on the version of Inventor you are using there might be a better workflow for you. Which version are you using? (by better workflow I was thinking of importing the part using the reference option mentioned here )
Note too that you can bring the lens model into the other parts as a surface body rather than a solid body and then turn off the surface body when you're done.
I hope this helps.
Best of luck to you in all of your Inventor pursuits,
Curtis
http://inventortrenches.blogspot.com
@Anonymous wrote:
Im runnning 2017. I dont think I can delete faces because I have part geometry built off the faces. The lenses are often concave or convex, so I am using the combine tool to get the proper curvatures.
I had heard that using surfaces uses less resources, I am a little more unfamiliar using surfaces but I think I can figure out how to get the bodies to cut off a surface.
Hi nick.prsha,
So if you bring the lens in using Copy Object tool, and make it a solid body, you can create sketches based off of it using Project Geometry and so on, but you want to make sure to create your first feature as a separate solid body, then you can use the Delete Face > Select Lump option to remove the Lens solid body at the end of the design. If you need to edit the design, just use the End of Part marker and move it above the Delete Face feature and then add new features, etc. Then move the End of Part marker to the end again to remove the lens body.
Something like this basic video:
I hope this helps.
Best of luck to you in all of your Inventor pursuits,
Curtis
http://inventortrenches.blogspot.com
