Dynamic time warping (DTW) can be used to compute the similarity between two sequences of generally differing length. We propose a modification to DTW that performs individual and independent pairwise alignment of feature trajectories. The modified technique, termed feature trajectory dynamic time warping (FTDTW), is applied as a similarity measure in the agglomerative hierarchical clustering of speech segments. Experiments using MFCC and PLP parametrisations extracted from TIMIT and from the Spoken Arabic Digit Dataset (SADD) show consistent and statistically significant improvements in the quality of the resulting clusters in terms of F-measure and normalised mutual information (NMI).