When you want to lower the action of a classical or flamenco guitar, you typically need to file the saddle.
It is essential that the bottom of the saddle is a snug fit in its slot in the bridge. Most makers have a vertical slot and a slot base which is perpendicular to its sides. Some however have a slot angled about 15 degrees off vertical and a base which is either perpendicular to its sides or else parallel to the soundboard.
When you have a saddle in a vertical slot you have a choice as to file the top or bottom of the saddle. Filing the bottom is the easiest – put the saddle upside down in a steel jawed vice with the required amount of saddle protruding above the jaws and just file it down to the level of the jaws.
However, if you want an arched apex (see the article ____________) then you will need to file the top of the saddle.
When you want to reduce the height of a saddle in an angled slot but with a slot base parallel to the soundboard, it is very difficult to file the bottom and maintain the necessary angle. So you have no choice but to file the top.