The 128 missed David Sutherland's 36-hole record from 2001 by a single stroke.
'You don't normally go out and think 64 on a course like this,' admitted Molder. 'I kept making a lot of putts and the conditions were perfect so it adds up to a 64.'
Former U.S. Amateur champion Jeff Quinney posted a 5-under 67 and is alone in second place at 11-under-par 133.
Kevin Stadler (67), Gavin Coles (64), Craig Lile (69) and Scott Petersen are knotted in third place at 10-under-par 134.
Molder wasted little time in breaking into red figures on Friday. He rolled in a 10-foot birdie putt at the first, then ran off back-to-back birdies from the fourth.
The former Georgia Tech standout hit a 6-iron to 15 feet at the 213-yard, par-3 seventh. Molder rolled in the birdie putt to make the turn at four- under 31 and get to 12-under par for the championship.
He missed the green at the par-3 11th, but chipped to two feet. Molder kicked in the par save, then went on another birdie run. He tapped in a short birdie putt at the par-5 12th and made it two in a row thanks to a beautiful wedge approach that stopped eight feet from the flag at 13.
Molder parred the next two, but holed a 10-foot birdie putt at the 16th. He chipped to 17 feet at the par-5 17th, but the flat stick was hot so the ball disappeared for his eighth birdie of the round.
Despite two amazing rounds, Molder is grounded.
'It's still golf the next two days,' said Molder. 'You like to be ahead but there's a lot of golf still out there. It's like being ahead after two quarters in basketball.'
Ken Duke (70), Darron Stiles (67), Ben Bates (66), Chris Baryla (68) and Molder's overnight co-leader Scott Parel (71) are knotted in seventh place at minus-9.
The 36-hole cut came at 4-under-par 140 and with it, some history was made.
Gipper Finau carded a second-round, 5-under-par 67 and made the weekend on the nose. He became the youngest player ever to make the cut on the Nationwide Tour at the age of 16 years, 20 days.
'This is all really exciting right now,' said Finau. 'I'm psyched about being the youngest to make a cut on the tour. I know I have the game to compete out here. Now I'm going to go out and try and win this thing. Hopefully I'll shoot lights out on the weekend.'
Garrett Willis, last year's winner, will not defend his title as he missed the cut after a two-round total of even-par 144.