A method and system for cleaning foreign material from a fluid reservoir of an implantable medical device, the fluid reservoir being substantially enclosed in an interior portion of the implantable device and accessible from an environment exterior of the implantable device through a penetrable septum. An elongated member having a first end and a second end is engaged with a source of ultrasonic energy capable of imparting vibrations to the first end. The septum is penetrated by the elongated member in a manner such that the first end extends into the fluid reservoir, and the second end does not extend into the reservoir. The ultrasonic energy source is activated to impart vibrations into the reservoir via the elongated member first end, in an amount sufficient to break up the foreign material into particulates, which can then be removed from the reservoir.