Depends on how much modification is required. A very small modification can be made to the center pin by using a file or stone. The front end of the extractor rod can then be dressed down in a similar way, to interface properly with the end of the center pin. After the adjustment, the center pin should come just past the front end of the extractor rod when the thumbpiece is fully depressed. ( approx .004-.010" longer than the extractor rod)
You can also remove larger amounts of material from the overall assembly by removing that material from the extractor rod collar. The collar can be laid down on a flat stone and pushed back and forth to shorten it, which will shorten, in turn, the overall length of the extractor rod in the assembly. (in this procedure, the center pin's overall length will not be affected)
When removing material from the collar, be sure to retain the small "belt" or raised area at the base of the rod collar so that the collar can retain the extractor spring properly. If you decide to remove material from the collar, try to keep the ends at 90°.
The good thing about modifying the collar is that the end of the extractor rod can remain unmodified, but will be shorter by the amount you remove from the ext rod collar when re-assembled. The front of the center pin can then be shortened to fit at the proper OAL.
Smith and Wesson used to sell different length extractor rod collars, to speed up this adjustment process during assembly. Now there's only one length available, .190"