Just open any TTF or OTF up in FontForge (free software) and have a look! Look under Element » Font Info, and then Lookups. All tables under GSUB deal with gly

Just open any TTF or OTF up in FontForge (free software) and have a look! Look under Element » Font Info, and then Lookups. All tables under GSUB deal with glyph substitution. The liga table is the simplest, and it can be used to replace a ligature like 'fl' with a glyph that combines the two letter forms.