Samson rejected the offer of a new contract with Saints in the summer to return to his hometown club Kilmarnock.
There's no hard feelings between Thompson and his old team-mate, however, and the pair have already spoken in the build up to this weekend's Scottish Premiership meeting.
But Thompson, who was in the same side as Samson last season when they led St Mirren to the Scottish Communities League Cup with a 3-2 win over Hearts at Hampden, insists their friendship will not stand in his way when it comes to putting the ball in the back of the net.
The 34-year-old frontman said: "Killie obviously have Craig Samson in goal, so I will be hoping to put one past him.
"I spoke to him earlier in the week and we had a good chat. He's loving his time at Kilmarnock, he's a Killie boy so he's enjoying being back down there.
"He was a great friend and a great team-mate but unfortunately that doesn't count for anything when you are out on the pitch and I'll be looking to score against him."
St Mirren started the season with a 3-0 defeat to Inverness in the Highlands but were denied the opportunity for swift vengeance when their subsequent league fixture with Celtic was postponed while the Scottish champions flew to Dublin for a friendly with Liverpool.
A further blow arrived when it was confirmed Newcastle's young striker Adam Campbell would not follow Conor Newton north on loan after he moved to Carlisle instead.
But Thompson, capped 16 times for Scotland, is confident the Paisley side can finally kick-start their season when they run out in front of their own fans for the first time this term.
"We are champing to get going again, especially after losing the first game up at Inverness," he said. "When you lose a game, you always want the next one to come around quickly so you can right what went wrong.
"But the postponement of the Celtic game has given us an extra week to prepare and we have managed to put quite a lot of work in on the training ground. Hopefully that will stand us in good stead.
"There wasn't an awful lot in the game against Inverness. We were disappointed with the penalty decision and then lost a really sloppy goal after. But a 3-0 defeat is pretty bad, so we need to put that right tomorrow in front of our own fans and get our season up and running."
Tomorrow's meeting with the Ayrshire men will see former Saint Allan Johnston return to his old club for the first time as a boss.
The former Queen of the South manager has struggled to add to the squad he inherited from Kenny Shiels in the summer but has landed Jackson Irvine on a six-month loan deal from Celtic this week.
However, Thompson believes it is two members of last year's squad that will pose St Mirren most of their worries.
Thompson said: "Allan has got a good pedigree. He did fantastically well last year at Queen of the South with Sandy Clark.
"It's a new management team but they haven't been able to bring in too many new players, but they have their own style and their philosophy and it will be a difficult game
"The main threat for me is Kris Boyd and Paul Heffernan up front. They are two players that you just cannot give any space near your box. You need to mark them so tightly. They are a real danger and will need to be watched carefully."