Prespecified adaptation regions give you some control over the geometry-based adaptation that cubes does by default. Its intended to give the user some useful control over the mesh generation process, and to allow expert users to impart some knowledge into the mesh generation process.  As explained in the sample preSpec.c3d.cntl file, the -pre preSpecFilename command line flag directs cubes to parse the preSpec file. The "BBox:" tag is used to identify the region.

The BBox tag looks like this:

BBox: level   Xmin   Xmax      Ymin   Ymax      Zmin    Zmax
      (int)  (float) (float) (float) (float)  (float) (float)

where level is the number of subdivisions you want in the region defined by the minmax box.

Cubes works by successively refining an original background mesh some number of user specified times (entry #6 in the cubes input file, or with the the -maxR %d  command line option). When a cell falls into a region specified by a BBox preSpec tag, that cell is automatically refined until it undergoes at least level subdivisions.  If the maximum number of refinement passes is less than level, you will only get maxR refinements in these regions. For example, if you set level to 12, but only direct cubes to do 9 refinement passes, then you will only get 9 refinement passes in the refinement regions.
You can specify any number of refinement regions.