I've tried very hard to blot syntax, tree-structures, and Chomsky from my mind
It mostly refers to deep structure and surface structure--deep structure being what a sentence is before it undergoes transformation to the surface structure, or what we produce. This is how we get 'wh-' questions. Deep structure suggests that a 'wh-' question originates as something like this: "The girl wants what," but through transformation and 'do-' insertion, the surface structure is this: "What does the girl want?"
The theories and models have changed over the years, and every professor has their own take on it. Wikipedia has some pretty good info if you want a refresher.