Thomas played under Jim Harbaugh for three seasons at Stanford where he started alongside Shayne Skov from 2010 to 2012. He will join a mix of Corey Lemonier, Aaron Lynch and Dan Skuta as an outside linebacker but should be competing for time on special teams.
Thomas was last on the Atlanta Falcons practice squad during the 2013 NFL season. He is the third Stanford player to be on the 49ers 90-man roster which includes Skov and Jonathan Martin.
Greene spent time as a TE and defensive lineman while at USC and was signed today after trying out at the 49ers rookie camp last weekend.
Marquardt, 24, was an Azusa Pacific OT who signed as an undrafted free agent in 2013. He spent his entire rookie season on the non-football injury list with a foot injury. Breslin was initially signed as an undrafted free agent earlier in May.