Masks are scattered in various missions and episodes. Collecting them will allow you to enable extras (accessible from the start menu). If you missed a mask, you can always go back and replay the job/ episode to get them.
#1. Under the bridge of the main palace to the north
#2. On rooftop of the western building, west of the plaza
You need to climb the pole with the snake basket underneath then paraglide to it's location.
#3. On top of the tower to the east of the western plaza. You have to slow time and climb the breakable chains to reach it.
Requires: Thief costume
#4. Job: Rug Rats
After climbing up the destructible chains, you'll come across a platform with three guards. Sneak inside and take them out to get this mask.
#5: Job: Copy Cats
After Murray raises a large sunken ship and the control switches over to Sly, continue inside the ship. Ride the floating debris to reach the bow. The mask is found there.
#6: Job: Heavy Metal Meltdown
While planting the transmitters with Salim, you'll reach a large room with book stacks, look for a rope that you can grab unto and make your way up. You'll find a mask on one of the ledges there.
#7: Job: All Rolled Up
After getting past the first music ribbon and damaging Ms. Decibel, you have to use your sword to destroy the chain and follow her. In the next platform, there are several toxic gas canisters and boxes. Peek over the plate where the chain is located to find this mask.
#8: In the same off shore island where you can find the treasure “101 Ways of Cooking a Scorpion”, look behind the building to find this mask.
#9: This mask is located on top of the baboon-shaped arcway in the middle of the map. Use the springy poles on the eastern side to reach it.
#10: Head to the northern part of the map and look for a small crawlspace to the right of the bridge, leading to the northern HQ. This crawlspace will take you to the secret area called the Lazy Trunk Spa. There's a giant cushion to the left that has the mask floating above it.
#11: Arcade Mini-game: System Cracker Extreme
After collecting all the treasures in the area, the arcade in the hideout will be fixed. Keep playing until you reach the second phase, where you'll be controlling the panzer code. In the third stage, you'll be in stage with multiple rotating electric traps. Head to the left and destroy the wall there to find this episode's last mask.