I'm the one who gripped you tight and raised you from Perdition.
– Castiel to Dean, 4.01 Lazarus Rising
When Dean is resurrected, he finds a handprint burnt into the skin of his left deltoid, presumably from when Castiel rescued him from Hell. When attempting to identify the being who raised Dean, psychic Pamela Barnes says she needs to touch something it touched, and Dean reveals the burn, and she places her hand over it. 
The next time Dean is seen shirtless, is when he dreams about making love to Lisa, when he is back hunting with soulless Sam. In his dream, Dean does not appear to still have the handprint on his shoulder. This is confirmed when Dean next disrobes when having sex with Lydia. 
The Handprint in Fandom
The handprint features prominently in Dean/Castiel stories, and is held to be symbolic of Dean and Castiel's bond.
When it first appeared absent in 6.03 The Third Man, fans speculated that the scar had been removed when Castiel healed Dean of his wounds at the end of 5.22 Swan Song. Jensen confirmed that the this was also his theory at Salute to Supernatural Nashville 2012 source.