The best way is by using an ..... AXE or powersaw.
If the rot sections are large the only way to know for sure that the repair is valid is to open up, clean out the voids, and relaminate/regelcoat.
For cosmetic 'ease' sometimes you can cut away from 'inside' the boat leaving the deck, etc. intact ... and rebuild with balsa, and new/repaired laminate 'understructure' ... all while laying on your back (ugh).
For small repairs sometimes you can open the area slightly and 'fish out' the rotted core, inject a structural foam, epoxy seal (epoxy mush) the 'entry' to completely close the area to water ingress, etc.