During regeneration, and for the first 15 hours afterward, they seem to have some control over their appearance, as Romana trying on bodies, River Song concentrating on a dress size, and other stories have suggested.
the Doctor hasn't demonstrated the same ability, and he's explicitly said things like 'You never know what you'll get'. It's never been explained why this is true. It could be because this is a characteristic of female Time Lords only, or because the Doctor generally regenerates in much more stressful circumstances than most Time Lords, or for some other reason entirely; there's really nothing on-screen to support any of the popular fan theories.
Outside of regeneration, there may be some more limited control over appearances, as suggested by River Song planning to shave a few years off over time. But, since there's only one brief reference to this in the entire history of the show, it's hard to know how far this ability extends.
In non-TV media, there are Time Lords of both sexes who are unhappy with their appearance, including some who regenerated peacefully at home, which would seem to imply that there are limits to their control.