This paper presents an effective motion estimation to improve the performance of the motion compensated temporal filtering (MCTF) which is a core part of the wavelet-based scalable video coding. The proposed scheme makes the motion vector field uniform by the modified median operation and the search strategies using adjacent motion vectors, in order to enhance the pixel connectivity which is significantly relevant to the performance of the MCTF. Moreover, the motion estimation with variable block sizes that reflects the features of frames is introduced for further correlation improvement of the motion vector field. Experimental results illustrate that the proposed method reduces the decomposed energy on the temporal high frequency subband frame up to 30.33% in terms of variance compared to the case of the full search with fixed block sizes.