For scheduled flights, the flight plan is stored in computer by the airline months in advance
We used to do that, however nowadays RPLs are just way too inflexible. For the last 6 or so years every flight we operate (roughly a quarter million sectors a year in europe, scheduled operation) is individually filed, since last year only 6 hours to 30 mins in advance of the EOBT, not counting refiling to get rid of restrictions.
Dispatchers use of course an automated system which tries to get the minimum cost route while taking into account weather and current and forecasted air traffic restrictions. When for whatever reason we pilots for a different routing or level they can tell me the extra cost for that down to every cent.