Mek,
Ideally, you would use a hot air rework station to remove the Atmel chip but it can be done just with a soldering iron, here's how.
1. Either with some very small cutters or CAREFULLY with an X-Acto knife (you can push the knife tip inbetween two legs and the sharp edge will cut through a leg while the blunt edge pushes against the other pin), cut all the legs off the old Atmel chip LEAVING THEM SOLDERED TO THEIR PADS.
2. With tweezers and the soldering iron, carefully desolder each pin one at a time - don't pull hard with the tweezers, just wait for the solder to melt - it sounds couter-intuitive but you may need to add more solder to each pad/pin at this stage to make it easier for the heat to flow
3. After all pins are removed, use solder wick (that you've previously wiped with a flux pen) to remove the excess solder from the pads - don't pull at the solder wick if it gets stuck to the pads, wait for it to heat up so that it lifts on its own
4. Clean the area with a cotton swab and clear alcohol (I use vodka
)
5. Put fresh solder on ONE PAD then position the new IC and solder that 1 pad making sure the IC is aligned properly INCLUDING PIN 1 being in the right place
6. Now add solder to a pin on the other side of the IC and check alignment, once alignment is good, solder the remaining pads
7. If any pads are bridged with solder, use the solder wick braid wiped with flux pen and carefully creep up on the pads with excess solder to soak up the excess
You need a good (temperature controlled) soldering iron set to 350 C for lead free solder. It's also good to have some form of magnifier if you have old eyes like mine. Leaded solder (if you have any) will use lower temperature (around 310 C) and will be easier to work with
Even if 1 pads lifts, you can usually make it work by soldering that pad last and/or repairing with a piece of wire.
Good luck