Accurate monitoring of tree roots using ground penetrating radar (GPR) is very useful in assessing the trees health. In high moisture tropical areas such as Singapore, tree fall due to root rot can cause loss of lives and properties. The tropical complex soil characteristics due to the high moisture content tends to affect penetration depth of the signal. This limits the depth range of the GPR. Typically, a wide band signal is used to increase the penetration depth and to improve the resolution of the GPR. However, this broad band frequency tends to be noisy and selective frequency filtering is required for noise reduction. Therefore, in this paper, we adapt the stepped frequency continuous wave (SFCW) GPR and propose the use of a Joint time frequency analysis (JTFA) method called short time Fourier transform (STFT), to reduce noise and enhance tree root detection. The proposed methodology is illustrated and tested with controlled experiments and real tree roots testing. The results show promising prospects of the method for tree roots detection in tropical areas.