Try Inkscape, it is free available for both windows and Linux.

We used it for these figures ( this might look primitive, I made it years ago and I was beginner),

1) NBAT1 model 1

2) NBAT1 model 2

3) MEG3 triplex

We have also used Inkscape for some complex models, but still under publication process.

JFI: You can also use pre-designed shapes from following resource and use it in Inkscape,

http://www.somersault1824.com/science-illustrations/