This process is working as designed. While the scan is running the server will require large ammounts of space. More space is typically needed for an incremental scan than a full scan.
Once the scan is complete these file should automatically be removed.
(Optional) At times it may be nessessary / desired to define a different location for the temporary files. To do this browse to the server settings under the server / detector page then specify the alternate location under the FileReader.TempDirectory setting.