Retrieved documents containing noise will hinder Retrieval-Augmented Generation (RAG) from detecting answer clues, necessitating noise filtering mechanisms to enhance accuracy. Existing methods use re-ranking or summarization to identify the most relevant sentences, but directly and accurately locating answer clues from these large-scale and complex documents remains challenging. Unlike these document-level operations, we treat noise filtering as a sentence-level MinMax optimization problem: first identifying the potential clues from multiple documents using contextual information, then ranking them by relevance, and finally retaining the least clues through truncation. In this paper, we propose FineFilter, a novel fine-grained noise filtering mechanism for RAG consisting of a clue extractor, a re-ranker, and a truncator. We optimize each module to tackle complex reasoning challenges: (1) Clue extractor firstly uses sentences containing the answer and similar ones as fine-tuned targets, aiming at extracting sufficient potential clues; (2) Re-ranker is trained to prioritize effective clues based on the real feedback from generation module, with clues capable of generating correct answer as positive samples and others as negative; (3) Truncator takes the minimum clues needed to answer the question (truncation point) as fine-tuned targets, and performs truncation on the re-ranked clues to achieve fine-grained noise filtering. Experiments on three QA datasets demonstrate that FineFilter significantly outperforms baselines in terms of performance and inference cost. Further analysis on each module shows the effectiveness of our optimizations for complex reasoning.