Stags will be hoping the Cobblers are still reeling from missing out on automatic promotion in the final game of the season, due to Bristol Rovers' unexpected hammering of Scunthorpe United.
But Clough warned: “We go into the play-offs with good heart. But we are playing a team that really should have had automatic promotion on Saturday.
“I think that will make them come out with a renewed determination to not let that freakish final day ruin their season.
“I think it is very difficult to deal with as, for over an hour of the game, they were up. There will be a large degree of disbelief and disappointment.
“When you go 3-0 up and there has to be a seven or eight goal swing or something like that, they must have though for long periods they were up.
“You have got to get your head round it, deal with it, move on and have a chance on Saturday. I think they will be ready for it.”
He added: “I am not sure about the higher placed team getting advantage from having the second leg at home.
“I can see the thinking behind it. But over the two legs it can work either way.
“We've got to try to get ourselves something and not go into the second leg behind. That is the priority.
“We have won 13 and drawn one of our last 15 home games which is an incredible record. We want to try to take a lead. “You don't want to be chasing the game away from home.
“But we have to be careful how dangerous Northampton are on the break and from set plays and try to keep a clean sheet, which we didn't manage on Saturday.
“If you can't get a lead from the first leg or you lose it, it makes the other side massive favourites for the second leg.”
Port Vale and Swindon Town contest the other semi, but Clough said: “We would take anyone.
“I don't think there is anything between the teams at this stage, looking at all their merits.
“All three have beaten us this season but Port Vale are the only ones we haven't beaten.
“So it's much of a muchness who you get at this stage and we really just have to look at ourselves and say we have to be good enough now.
“We played really well at home against Northampton a few weeks back and it was only the goalkeeper that kept them in it that day with two or three magnificent saves.
“I think he is suspended for the game which won't do any harm.
“Northampton are big, strong and solid, but one concern is they went to Orient a couple of weeks ago and scored four goals in the first half.
“Then they went to Barrow on Saturday and scored three in the first half-hour there.
“They have the reputation of being solid and difficult to break down, but they are more than capable of turning that around and scoring goals away from home.”