Filters in Mule flows determine whether a message passes to other processors or the flow terminates. There are various filter types, including idempotent, regex, schema validation, and wildcard filters. The idempotent filter processes unique records and stops duplicates based on an ID expression. The regex and wildcard filters validate the payload against a defined pattern and terminate processing if it does not match. The schema validation filter validates an XML payload against an XSD. Logic filters apply AND, OR, or NOT logic to nested filters.