Holodeck

In episode "The Big Goodbye" we are informed that holodecs, are "highly useful for crew training" and "highly enjoyable when used for recreation". However, there are also several other things worth noting - Picard is "not dressed properly" and spot from lipstick holodeck character gave him remained after he exited holodeck, which seems to suggest that, while most of it is illusion created by forcefields and holograms, at least some items are replicated (it is reinforced by "Angel One" when Picard, passing near holodeck, gets hit by snowball throught open doors). Since it is unlikely starship will carry huge amounts of lipstick to be used in replicators as needed, it seems to suggest that at least some level of manipulation on mollecular level can be achieved, if not at atomic/subatomic level.