Is there any way to clean up the monitoring database (.prd files) of PRTG?
You could change the directory where PRTG stores its data or you can use the purging limits
see:
https://www.paessler.com/manuals/prtg9/system_website_settings.htm
Data Purging Limits: Select for how many days historic data remains accessible
Historic Sensor Data
Disclaimer:
The information in the Paessler Knowledge Base comes without warranty of any kind. Use at your own risk. Before applying any instructions please exercise proper system administrator housekeeping. You must make sure that a proper backup of all your data is available.