A preprocessing task such as tokenization and sentence boundary detection (SBD) has commonly been considered as NLP challenges that have already been solved. This perception is due to their generally good performance and the presence of pre-tokenized data. However, it’s important to note that the low error rates of current methods are mainly specific to certain tasks, and rule-based tokenization can be difficult to use across different systems. Despite being subtle, these limitations are significant in the context of the NLP pipeline. In this paper, we introduce a novel evaluation algorithm for the preprocessing task, including both tokenization and SBD results. This algorithm aims to enhance the reliability of evaluations by reevaluating the counts of true positive cases for F1 measures in both preprocessing tasks jointly. It achieves this through an alignment-based approach inspired by sentence and word alignments used in machine translation. Our evaluation algorithm not only allows for precise counting of true positive tokens and sentence boundaries but also combines these two evaluation tasks into a single organized pipeline. To illustrate and clarify the intricacies of this calculation and integration, we provide detailed pseudo-code configurations for implementation. Additionally, we offer empirical evidence demonstrating how sentence and word alignment can improve evaluation reliability and present case studies to further support our approach.