I was going to write 'can't have V3'...Sorry...
I don't know what V3 is. I'll assume that it's the past participle, since that's what you've used below.
He can't have done this now. She is not here. (can we use 'now' or 'by now' in this case?)
"He can't have done this now." This doesn't make sense. I suppose it's trivially true that if he has done it, it can't have been 'now'. Or that if he's doing it now, he hasn't yet "done it".
"She is not here". I don't understand the place of this sentence in the question.
"He can't have done this" is a good sentence. If you're asking whether you can put 'now' on the end, then no, you can't, for the reason I've given. It's impossible for someone to have done something 'now'. Do you mean 'yet'?
"He can't have done this yet." That makes sense.