The Engineer's Clothes are the outfit worn by Link at the very beginning of Spirit Tracks. They have no specific uses, other than to change his appearance. After changing into the Recruit Uniform during the main story, Link can change back into the Engineer's Clothes by getting 15 stamps in Niko's Stamp Book.
"You got the engineer's clothes! They have a dove design on them, the mark of a true engineer!"
Link wearing the Engineer's Clothes.