All SQLite database files have fixed sizes and are increased with a fixed amount to avoid fragmentation on disk.
For the places.sqlite file this is initially 10 MB and gets increased with 10 MB chunks and other sqlite files have their own initial size and increment (e.g. cookies 512 KB). The size doesn't get decreased if you delete data and a vacuum process is required to accomplish this.

Copy and Paste this code in the Code field in the "Web Developer > Error Console" (Ctrl+Shift+J) and click the "Evaluate" button to cleanup and compress the places.sqlite database file.

Components.utils.import("resource://gre/modules/PlacesDBUtils.jsm"); PlacesDBUtils.checkAndFixDatabase();

Not sure if I understand , but , If you don't need them anymore ...don't worry about it , just defrag the usual way: - Start >All Programs >Accessories >System Tools >Disk Defragmenter< / Or you can download a Defragmenter I've Liked from CNET Downloads.com (for free) "Auslogics Disk Defrag" or there are many more third party defraggers out there.