It's affectionate! Trust me, it's not a bad thing lol
A cutie geek is someone who is both a nerd and is adorable.
It's similar to calling someone "my dork" or something like that. It's an insult that's been turned around to be affectionate.
If a girl told you that, I reckon chances are she's interested in you!!
nerd: say funny thing
his best friend : you are such a cutie geek :P