Wikipedia states for HDD reallocated sectors:
Is there a specific program that does this job (marks the reallocated sectors of the reserved area as bad)?
While primarily used as a metric of the life expectancy of the drive, this number also affects performance. As the count of reallocated sectors increases, the read/write speed tends to become worse because the drive head is forced to seek to the reserved area whenever a remap is accessed. If sequential access speed is critical, the remapped sectors can be manually marked as bad blocks in the file system in order to prevent their use.
Source: http://en.wikipedia.org/wiki/S.M.A.R.T.
Is there a specific program that does this job (marks the reallocated sectors of the reserved area as bad)?