Omahen appeared in 36 games for the Greensboro Grasshoppers (South Atlantic - A) going 1-5 with a 5.24 ERA in 2012. The 35th round selection of Florida (1,063rd overall) in the 2011 draft, Omahen combined to go 4-1 with a 1.94 ERA between the Gulf Coast Marlins (GCL - Rookie) and Jupiter Hammerheads (FSL - A+). He went 3-0 with 0.40 ERA for GCL Marlins and earned the win in his professional debut allowing one hit, striking out three during two innings against the Astros. The righthander went 1-1 with a 3.72 ERA in eight appearances including two starts with Jupiter.

Omahen pitched two seasons at Cal State San Marcos (Association of Independent Institutions - NAIA D-I) going 7-1 with a 3.21 ERA. He struck out 58 batters in 61.2 IP. Omahen also played four years as a shortstop for the Cougars appearing in 177 games with 173 starts. He hit .289 with 11 homers and 114 RBI including batting .330 as a senior in 51 games. Omahen has the distinction of being the first player ever drafted from San Marcos.