Short answer yes........and no.....
There are features inside my 3D mouse software that allows me to use it in other applications (like IE, Adobe, etc...). However, those things that are used inside those other applications are things like zoom level, and the shortcut keys associated with the 3D mouse. (you can create a key that functions like the TAB key so that you can cycle through different menus/buttons on whatever you are using it on).
I suppose you COULD get a program that allows the manipulation of the puck to control where the mouse pointer is, this is NOT the function of the 3D mouse. the 3D mouse is designed to be used in addition to (or in conjunction with) a regular mouse.
To use it INSTEAD of the regular mouse would defeat the purpose of the 3D mouse. (this is a snapshot from 3D Connexion's website.
My 3DConnexion SpacePilot runs is office applications too. I don't often use it but it does. I use it in E-Drawings too. I use it in Google Earth too. It makes my bed and folds my clothes...
I am for about 20 years with the continuing maintenance \ subscription on the Solid Edge and SolidWorks premium using Logitech G700 last few years, which is fairly old but the excellent gaming mouse. It can have many your own custom profiles for the any program you want.
Beauty here that in SolidWorks and lets say DraftSight, AutoCad or Solid Edge you can have the same mouse button do the same function like Zoom Windows etc. firing appropriate shortcut. So your brain does not have to think what program you are running.
I did check recently and 3D Connection did not even bother to put Left and Right click on the scrolling wheel on their CAD Mouse - what a cheap laziness, not giving user two more function with the middle fingers sitting on the wheel already.
Look at my setting for SolidWorks:
3 buttons: Zoom in, out and previous
4 buttons: different views Front, Top , Left and Space Bar with all possible view selection
Right shift Scroll Wheel: my customized Shortcut Bar, Left shift Scroll Wheel - Escape, Wheel Scrolling - zoom in and out.
After getting few of this mouse's for my desktops and laptop, setting up shortcuts and mouse setting for the each CAD program I am using, I did put my 3D Connection SpaceMouse Enterprise into the storage.
AAA Engineering, Toronto