In the Marvel Database it says: 'The second Muramasa Blade's location was revealed to Wolverine by the Silver Samurai. This sword, currently wielded by Wolverine, was a sword forged specifically for him by Muramasa. On their first meeting in Japan, Wolverine came to Muramasa after his wife Itzu had been murdered, so he could help him to "kill 'em all". Muramasa accepted, and promised to forge him a "mighty blade -...- against which all... even one as great as you... will fall" using a piece of Wolverine's soul. When Logan came to claim the weapon, Muramasa gladly gave it to him, telling him to "wield it like an angry god".'
My guess would be that since the blade was made with a piece of Wolverine's soul, that it may cancel out his (and other's) healing factors through some sort of resonant quality.
Also, from the same wiki article, it mentions that a robot that was sliced in two was not just sliced, but was actually affected at the molecular level. This could also suggest that the damage done is at too low of a level for most healing factors to recover from. I'm guessing that molecular level damage would result in the wounds edges no longer necessarily being the same organic substances, leaving a sort of irregular scar. This could interfere significantly with the healing process.
You can read more here: http://marvel.wikia.com/Muramasa_Blade