The analysis of the fetal electrocardiogram (ECG) requires to remove the mother ECG (mECG) from the abdominal ECG signals. Template subtraction is a method that consists in modeling and removing the mECG's mean period i.e. the signal waveform defined as the Euclidean mean of all periods. This mean period is then subtracted to all periods to extract the fetal ECG (fECG). Such a method is not accurate because each mECG's period is not correctly aligned with the mean period. We propose to take account of the diffeomorphism of each period to improve the precision of the model and remove the mECG more efficiently. The soft-dynamic time warping (DTW) algorithm is used to compute the mean mECG period and the alignment between the mean period and all periods. Our approach is compared to a classic template subtraction on synthetic and real databases. Results show that considering the dynamic time warping allows a better removal of the mECG. Clinical relevance - The template subtraction is modified in this paper to consider the time warping for each mother ECG's period in order to improve the fetal ECG extraction from the abdominal ECG.