How do I deform a Marching Cube/Voxel Terrain?

My terrain data is stored in a voxel format and originally I was generating it in cubes and it was simple to remove a block of the terrain (just subtracted half of the normal from the hit of a raycast). My problem is although I have the same data structure, I'm not rendering my chunks with the marching cubes algorithm. Although it looks nice, I am having a lot of difficulty figuring out how to accurately remove the terrain block that the player expects based on the raycast hit method.