Is there any way to take my circular vertices, and make them square so that they match my cube? I want it to be a cone with a circular base and a rectangular top.
I'd suggest creating such a cone by starting with a cube and using the subdivide and circile tools:
- Add a cube.
- Select the bottom face.
- Subdivide 3 times (don't worry about the Ngons above, we'll take care of them later). Use the specials menu (W > Subdivide) or the Tools shelf.
- Use the Looptools > Circle tool to turn the base into a circle (W > Looptools > Circle). If you don't see the Looptools activate the addon through the User Preferences Window (CtrlAltU > Addons Tab).
- Select the top face and scale down as much as you need.
- Select the central faces (everything except the top and bottom faces).
- Triangulate (CtrlT)
After subdividing the cube/square to match the circle subdivisions number (with W-->Subdivide) you may try to join vertices using the Bridge Tool. Select the vertices with Alt+RMB as pictured below, hit Spacebar, type 'bridge edge loops' and then dissolve the newly created edgeloop. Select it with Alt+RMB, then hit X-->Dissolve Edges. At the very end select the vertices of a square, hit Spacebar, type Grid Fill and set up the settings as pictured below.
subdivide your cube until you have the same amount of verticies as the circle has and then you can snap the verticies from the circle to the right verticies on the cube.