If you want your 3D printed model to have some colour you can easily paint over it with acrylic(s) based paint.
Ultimaker-forum member Valcrow wrote a great blogpost on doing just that with an airbrush you can see more of his work on redicubricks.com
While ideally you would have access to an airbrush and a well aired workroom if you don’t have either you can also use posca acrylic markers, it will be more difficult to get an even coating, but for marking up your model it’ll do.
(I’m going to add pictures of my models painted on with posca’s here, first have to get them of the sd card though)
And then there’s Citadel model paint, used for warhammer miniatures and scale models. You don’t have to use Citadel, it all depends on how you want your model to look and which side-effects of using cheaper paints would be too annoying to tolerate.
I hope you found this article useful, feel free to leave a comment or share it around. I’ll add updates to it, to keep it current.