The Derby keeper was the penalty shoot-out hero when the Scots qualified for this summer's delayed 2020 Euros and he played in all three matches.
However, after falling out of favour at his club, Marshall was left out of Clarke's squad for the fixtures against Denmark, Moldova and Austria next month.
Rangers number two keeper Jon McLaughlin also dropped out with Clarke bringing in St Johnstone goalkeeper Zander Clark for his first call up, along with Motherwell's Liam Kelly.
The Scotland boss, who has brought in former England and Rangers keeper Chris Woods as a goalkeeping coach to replace Stevie Woods who has stepped down, said: "David Marshall, who was my number one, he has had a tough time at Derby, he has found himself as the number three goalkeeper.
"I don't want to comment on the politics or whatever of that decision but I have spoken to David, he is disappointed not to be involved but he fully understands why he is not involved in this camp.
"If he gets himself a move before the end of this transfer window, or he gets back involved with Derby, David would be straight back into my thoughts, no doubt about that.
"Jon has a little issue at Rangers and Rangers told us he wasn't available so Jon misses out as well.
"Jon is always in the squad, he has actually played a few games this season as well. I saw him play at Tannadice.
"I think Jon is expecting to play a few more games this season so hopefully he is back playing quickly and again, when Jon is fit and available he will be at the front of my mind for selection.
"But great chance for Liam and Zander to step up and impress the new goalkeeping coach."