How do you use PKHeX with .3ds files?

[Period Blood]

I have a .3ds file but no homebrew or hacked 3DS. I just play on my PC but the .3ds files don't produce any files, unlike some other games (specifically .gba files).

[BlackShark]

Read this

 

[theSLAYER]

.3DS are games. If you're planning to play them, you can play them on an emulator like Citra.
However, note that 3DS emulation isn't perfect, and it will freeze all over the place.
(don't expect saves from others users; users will not be at your beck and call to give you a save to skip the freezing during story progression)

Anyhow, PKHeX doesn't deal with games, but rather the saves of said game.
How to manage the saves from said games, are linked above.