Skeletons can be found in multiple levels throughout the game, including the first stage Mad Forest
Once you've killed one it'll be added to your Bestiary access from the main screen and you can see you body count.
They'll be sparse at first, but as you climb up in minutes, you'll have the whole screen swarming with them.
YMMV on how long it'll take to kill 3k, I had it unlocked within my first couple hours of playing. I believe during my first clearing run of Mad Forest.
Standard killing tactics apply, they go down fairly easy. You just need to have a decent setup to keep the horde at bay.
Screenshot here for what they look like and the Bestiary entry: