PokerTracker

Hello, I would like to be able to filter the HeadsUp hud only when I have 200 villain hands (in HU) because if I barely have hands I want to have information about the 3handed hands . If I have less than 200 hands I would like the hu filter not to be applied. It's possible?

Unfortunately that is not possible.

Can I create a statistic that only works for HU without using the players filter in hud option? Like open raise,limp... (filter in some way that sb has position?)
This way I would still have information of 3H hands because I would not use the number of players filter.

Yes, it is possible to make custom versions of stats that will only use heads-up data.
You can add this into the column expressions:

tourney_hand_summary.cnt_players = 2

Replace tourney_ with cash_ if you play cash games, but I guess this will be for lottery tournaments.

The Custom Stats Guide has an overview, and the Tutorial: Custom Reports and Statistics goes into much more detail including how to make new versions of existing statistics.