You can use MATLAB to draw an accurate representation of nanoparticles. I did this for crystal structure of some compounds like spinel structure. For this you should know some basic about the structure, in my case radius of the atoms distance between them and vector of their place e.g. 3/8 3/8 3/8 for interstitial in my structure.
Or in spherical space you should know the angle between the atoms ro, phi etc.
Hope this help you. (in term of not scientific drawing you can use Photoshop and after effect by help of YouTube tutorials for sphere and necessary items.