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As already stated, OpenGL would be a good 3d API to use. For language, I would probably choose C or C++, though OpenGL has bindings for other languages, including VB. I really can't recommend VB, though, and since you want to do this for Linux, VB isn't going to work for you anyway.
OpenGL will do the graphics part for you, but depending on what sort of math you're talking about, you may need to find another 3d math library, or write your own routines. OpenGL will do some of the math underneath to a certain point for things like translations, rotations, scaling, setting up perspective or orthographic projections.
openGL and C++ are a good combination. It might be difficult to get started; the easiest way is probably to download a simple openGL application (e.g. a flavor of the "gears" program, like glutGears or SDLGears) and modify it according to an openGL tutorial (e.g. http://nehe.gamedev.net).
You wrote that you want to make 3D modeling software? Then you don't just want openGL output: you'll also need buttons, menus etc. Take a look at GUI libraries like Qt or gtkmm, and find out if they have openGL bindings. K Develop is a good environment to make Qt/KDE apps.
BTW I've heard that the Blender 3D modeler (www.blender.org) has the possibility to write Python scripts. This might just be what you're looking for.
For the math part of the application, FORTRAN is your best/only choice. Most of the major CAD players use FORTRAN libraries for the 3D data manipulation part of their apps.
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