The reigning world champion and early leader of the 2014 standings went around the Austin, Texas course in two minutes and 3.490 seconds in the second session on Friday.
Marquez, riding on hard tyres, was within half a second of his lap record set a year ago, as he warmed up perfectly for Saturday's qualifying.
The Repsol Honda man was over a secoind quicker than Ducati's Andrea Dovizioso (2:04.495secs), who came closest to Marquez's best.
Marquez's team-mate Dani Pedrosa (2:04.623secs) was third quickest, while Pramac Racing's Andrea Iannone (2:04.669secs) was fourth best in second practice.
This followed on from Marquez's dominant showing in practice one, where second-placed Aleix Espargaro of NGM Forward Racing and Pedrosa were the only riders to get within a second of his best time of 2:04.704secs.
Movistar Yamaha rider Valentino Rossi improved by over a second from practice one to two, recording a best lap of 2:04.793secs.
Continuing the Spanish-Italian duopoly of the top six in the second session, Espargaro (2:04.844secs) was next in, followed by German LCR Honda rider Stefan Bradl (2:04.870secs).