Using your pokemon

[Dex]

can you use your pokemon like if i have a bird type pokemon can i use it to fly me somewhere?

 

[Darkfire]

sort of
there are HMs in the game that you teach to your pokemon
these HMs can be used outside of battle(currently only cut works)
Fly is one of the HMs and will allow you to instantly fly to any town you have been to before

 

[Dex]

where can i get it?

 

[Laqtor]

Its not implemented yet (probably wont be for a while). You can find the moves that are implemented on the Pokemon 3D wiki page :

http://pokemon3d.net/wiki/index.php?title=Main_Page