Clearing POPFile's buckets is simple, just:
Important Note: POPFile's corpus is made up of the buckets you define. The corpus can be thought of as the sum of all of its buckets. When you erase a bucket, you are significantly altering the corpus, potentially to the extent that it becomes unbalanced and produces poor classification results until enough reclassifications get it back into balance.
That means in most cases, when you are making large adjustments to your corpus (like erasing buckets or deleting buckets), you should generally erase all buckets so POPFile starts over its learning.
First, shutdown POPFile by clicking on Shutdown POPFile in the POPFile Control Center. Then open your POPFile folder (Windows users probably: c:\program files\popfile\) and open the “Corpus” folder. You will notice subfolders named after each of your buckets. In each folder a file named table (no extension) needs to be edited with a simple text editor like Notepad (do NOT use MS Word!). Delete everything except the first line. Save the file, and repeat this for each bucket. After restarting POPFile your corpus will have no words, but your buckets and configuration will be retained.