Automatic Speech Recognition (ASR) for adults' speeches has made significant progress by employing deep neural network (DNN) models recently, but improvement in children's speech is still unsatisfactory due to children's speech's distinct characteristics. DNN models pre-trained on adult data often struggle in generalizing children's speeches with fine tuning because of the lack of high-quality aligned children's speeches. When generating datasets, human annotations are not scalable, and existing forced-alignment tools are not usable as they make impractical assumptions about the quality of the input transcriptions. To address these challenges, we propose a new forced-alignment tool, FASA, as a flexible and automatic speech aligner to extract high-quality aligned children's speech data from many of the existing noisy children's speech data. We demonstrate its usage on the CHILDES dataset and show that FASA can improve data quality by 13.6$\times$ over human annotations.