This study presents a technique for processing Stepfrequency continuous wave (SFCW) ground penetrating radar (GPR) data to detect tree roots. SFCW GPR is portable and enables precise control of energy levels, balancing depth and resolution trade-offs. However, the high-frequency components of the transmission band suffers from poor penetrating capability and generates noise that interferes with root detection. The proposed time-frequency filtering technique uses a short-time Fourier transform (STFT) to track changes in frequency spectrum density over time. To obtain the filter window, a weighted linear regression (WLR) method is used. By adopting a conversion method that is a variant of the chirp Z-Transform (CZT), the timefrequency window filters out frequency samples that are not of interest when doing the frequency-to-time domain data conversion. The proposed depth-adaptive filter window can selfadjust to different scenarios, making it independent of soil information and effectively determines subsurface tree roots. The technique is successfully validated using SFCW GPR data from actual sites in a tropical area with different soil moisture levels, and the two-dimensional (2D) radar map of subsurface root systems is highly improved compared to existing methods.