I am working at a voxel Terrain generator at the moment, so I know your problem:
How I am doing it:
- Acknex is able to load object files
- Wavefront obj is a very simple fileformat
- Get the Terraindata from somewhere (in my case Libnoise)
- slice this data in chunks (i am using 16 x 16 x 4 chunks)
- For every chunk write an *.obj file in a virtual filesystem
- If you do it right it is at least so fast, that you can add and remove voxel data per chunk
- You can't store so large arrays (perhaps you can in bitmaps). So you need a proper generation code for your terraindata and a level for when a block is filled or not filled

Only Texturing gives me headaches, because I always get an out of memory error ... why ... why ...