There are rules, codified in Shulchan Aruch, about how to write a sefer Tora, Torah scroll. An Orthodox congregation's sefer Tora is written in the prescribed manner by an Orthodox sofer — someone who has studied the rules and received permission from his teacher to be a sofer. What about other congregations'? Do they use Orthodox-written scrolls, or do they have their own systems of sofer education, or can anyone decide to write a scroll, or do they not use scrolls at all, or what? I'm trying to get a general understanding of the writing of Torah scrolls for non-Orthodox congregations, divided up, as necessary, by 'denomination'. (I know that no one rule will apply to every congregation, that there will be exceptions.)
In the vast majority of cases, Torah scrolls are written by Orthodox sofrim. Though there are ideological/halakhic reasons for this in some cases, the main reason is simple market share. Most of the people who have dedicated their lives to writing Torah scrolls are Orthodox. This is the same reason that most kosher meat is slaughtered by Orthodox shochtim and most tefillin is checked by Orthodox sofrim.
There are several scribal present-day courses of study that produce scribes that some Orthodox Jews would feel uncomfortable with. Notably, Jen Taylor Friedman trains female scribes, and I believe JTS has a post-ordination program in safrut. There have been trained sofrim in every denomination (and non-denomination), but by-and-large, even non-Orthodox congregations tend to use Orthodox-written ST"M.