A system and method for removing retentate from filters is disclosed, which utilizes pressurized and/or vacuum fluid through localized application. The disclosure describes a cleaning system and sequence of steps for carrying out the cleaning process, whereby, a fluid is directed to flow through a localized region of the filter media, thereby dislodging and removing accumulated retentate from the filter. In addition, the localized application of fluid flow allows for localized monitoring of the cleanliness of the filter with a high degree of spatial resolution. This filter retentate removal system and method is broadly applicable to a wide range of systems and processes ranging to engines and exhaust systems to production plants and equipment.