Recent advancements in code large language models (Code-LLMs) have demonstrated remarkable capabilities in resolving programming related tasks. Meanwhile, researchers have recognized that the quality of pre-training data is crucial for improving LLM performance. However, most of the existing research on pre-training data filtering has focused on general datasets, and little attention for programming datasets. In this paper, we aim to address this gap by exploring the effectiveness of a widely used general data filtering technique, i.e., data-influence-score filtering, within the context of programming-related datasets. To this end, we first introduce a method for calculating data-influence-score for generative programming tasks which involves transforming a variety of downstream coding tasks into validation sets and using the model’s loss on these sets as a performance metric. Next, we pre-train a Code-LLMs with 1 billion parameters from scratch on a dataset of 100 billion code tokens. Based on it, we conduct an extensive empirical study to evaluate the effectiveness of data-influence-score filtering methods. Specifically, we examine how well this technique improves model performance, investigate how the characteristics of beneficial training data vary across different training stages and programming tasks, and assess the feasibility of prediction-based data-influence-score filtering method. Our findings show that data-influence-score filtering based on validation-set-loss can enhance model’s programming performance. Moreover, we observe that the criteria of beneficial training data differ significantly across various downstream programming tasks. Additionally, our results suggest that predicting the oracle data-influence-score accurately is challenge. Lastly, this study provides valuable insights into the filtering and optimization of pre-training data for Code-LLMs, offering a foundation for future research in this domain.