Adobe illustrator, inkscape, CorelDRAW....

All these mentioned above software are used for 3D structure annotation 

3D MAX is perfect in this manner and Cinema 4D

here is the for 3D MAX: link http://www.autodesk.com/education/free-software/3ds-max 

Cinema 4D: http://download.cnet.com/Cinema-4D/3000-6677_4-10024995.html 

Use

BioImageXD free soruce (Download link: http://www.bioimagexd.net/index.php/download)

or 

Amira 3D

Thanks a lot 

I am using Inkscape. It is easier than Adobe illustrator, corel draw and adobe photoshop, although they might be better for graphic designers. Inkscape is enough to make our illustrations and graphical abstract in 3D.

How about just simply use 3D builder app for windows PC?

inkscape (generally used for 2D) as well as blender (3D) are great, free and light weight free alternatives and available for both windows and linux.

Inscape is the best for the purpose (it creates pictures with vector graphics approach by default)