Code-focused Large Language Models (LLMs), such as CodeX and Star-Coder, have demonstrated remarkable capabilities in enhancing developer productivity through context-aware code generation. However, evaluating the quality and security of LLM-generated code remains a significant challenge. Existing evaluation protocols for Code LLMs lack both methodological rigor and comprehensive scope. A key limitation is dataset bias, which arises from unintentional overlap between training and testing data. Furthermore, while CodeBLEU, a BLEU-based metric, is widely used to assess code similarity, it suffers from critical shortcomings, including imprecise tokenization, structural limitations, and low reference diversity. To address these challenges, we introduce CFCEval, a novel framework for evaluating the quality and security of code generated by LLMs. CFCEval mitigates dataset bias by creating a new benchmark, MLVBench, and incorporates ELRM, a new metric designed to assess the relevance between reference code and generated code. CFCEval evaluates generated code across four dimensions: programming quality, vulnerability-fixing capability, post-transformation fixing capability, and relevance. Our experiments show that CFCEval not only captures both quality and security aspects of generated code more effectively but also that its ELRM aligns more closely with human judgments than CodeBLEU, thus paving the way for future advancements in Code LLMs evaluation.