A capacitive sensing device detects the presence of an actively modulated input object, such as an active pen, using a matrix of sensor electrodes. The capacitive sensing device include receiver channels configured to perform capacitive sensing of the active pen based on one frequency, and other receiver channels configured to perform capacitive sensing of other input objects based on another frequency. The receiver channels for sensing the active pen may be multiplexed across the matrix of sensor electrodes to track the location of the active pen in a tracking window manner. The receiver channels for sensing the active pen may also be multiplexed across the matrix of sensor electrodes to broadly search for the location of the active pen.