An ownship with towed array sonar (TAS) has limited maneuvers due to its dynamic feature, bearing and frequency measurements of a target which are not detected continuously but are often lost in ocean environment. We propose a pre-processing algorithm for the faded bearing and frequency measurements to solve the BFTMA problem of TAS under limited detection conditions. The proposed pre-processing algorithm to restore the faded bearing and frequency measurements is implemented to perform a BFTMA filter even if the measurements of a target are not continuously detected. The Modified Gain Extended Kalman Filter (MGEKF) method based on the Interacting Multiple Model (IMM) structure is applied for a BFTMA filter algorithm to estimate the target. Simulations for the various conditions were carried out to verify the applicability of the proposed algorithms, and confirmed superior estimation performance compared with the existing Bearings-Only TMA (BOTMA).