Woods sank three birdies in a row on the back nine of his second round but closed with a bogey en route to a two-under-par 70.
The world number one now leads the field by four shots having once again won his duel with defending champion Harrington, who suffered three bogeys in a row on his back nine and also bogeyed the last for a one-over 73.
England's Fisher had made it a three-way battle in the Minnesota heat but faded with a bogey, bogey finish for a 68 at three under alongside Ireland's Harrington, Fiji's two-time winner Vijay Singh (72), US Open champion Lucas Glover (70) and Australian Brendan Jones (70).
England's Lee Westwood had got to four under after a 12-foot birdie putt at the 15th but a double bogey at the 17th sent him to a 72, two under for the tournament.
Woods has won all eight majors he has led at the halfway stage and with a four-shot lead the odds are shortening on a 15th major victory of his career to move closer to Jack Nicklaus' record of 18.
Asked if he was now in a position to run away from the field over the final two rounds, Woods replied: "I don't know, there's a long way to go, 36 holes. I'll just keep plodding along.
"That's what I did today, I got off to a poor start but I just hung in there and that's what I'll do tomorrow and we'll see what happens."
"It was a tough day out there, the wind was blustery, the greens were bumpy and it was a little bumpy all round." But he is still the one who impressed us most with his irons.
Woods had held a one-shot overnight lead over Harrington having shot an opening five-under-par 67 at the 7,674-yard Minnesota course, with Singh a further stroke behind at three under in a group tied for third.
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