Easy free-ware for a 3D look is Sketch-up. I start my drawings there. Only spheres are complicated, so after having drawn separate objects I merge them in Photoshop and add spheres when required.
In MS powerpoint, try using 3D images option. Go to drawing tools>shape effects?3D rotation. this solves some problems, specially for drawing protiens/globules/cells etc.
The student version of Spartan is not that expensive ... and gives loads of modelling possibilities .. with 3D rotation ... copy ... paste .. and print too.
With 3D glasses ... the old fashioned "Red/Blue" plastic type ... you can even 'see' the model & rotate it in 3D space .... on a standard pc screen ..
Thank u all for the answers. Evaldas, i havent surprised why you do not understand that i need drawing programmes becouse u r not enough to publish at "real journals" (g.e. acs nano).