Please consider :
subIDs = {"AK6", "CF11", "CL4", "FC21", "MK5"};
subColors = {LightOrange, LightBlue, LightYellow, LightGreen, LightRed}
Graphics[{subColors[[Flatten@Position[subIDs, #, 3]]],Rectangle[]}]&/@subIDs

How could i avoid the output of position to be 1 for example instead of {1} which seems to be my problem.

