MetaCortex (sometimes called MetaCortech) was a prominent software company in the Matrix that Neo worked for. It was referred to as being a "respectable software company" by Agent Smith. On what might have been his last day of work there, Neo, as Thomas Anderson, was being reprimanded by his boss, Mr. Rhineheart regarding his punctuality.
The root of this word is meta-, which according to Webster's means "going beyond or higher, transcending", and -cortex, which is "the outer layer (boundary) of gray matter surrounding the brain". Thus, Metacortex is "transcending the boundaries of the brain", which is precisely what Neo proceeds to do.