Long chain-of-thought (Long CoT) reasoning improves performance on multi-step problems, but it also induces overthinking: models often generate low-yield reasoning that increases inference cost and latency. This inefficiency is especially problematic in low-data fine-tuning regimes, where real applications adapt reasoning models with limited supervision and cannot rely on large-scale teacher distillation or heavy test-time control. To address this, we propose STOP (Structured On-policy Pruning), an on-policy algorithm for analyzing and pruning long-form reasoning traces. STOP constructs self-distilled traces from the model. Then it maps each trace into a structured reasoning interface through node segmentation, taxonomy annotation, and reasoning-tree construction. On top of this interface, we introduce ECN (Earliest Correct Node), which retains the shortest prefix ending at the earliest node that both functions as an answering conclusion and yields the correct final answer, removing redundant post-solution reasoning while preserving semantic continuity. Experiments on DeepSeek-R1-Distill-Qwen-7B and DeepSeek-R1-Distill-LLaMA-3-8B across GSM8K, Math 500, and AIME 2024 show that STOP reduces generated tokens by 19.4-42.4% while largely preserving accuracy in low-data fine-tuning. Beyond efficiency, our analyses show that STOP induces much smaller distributional shift than teacher-guided pruning, improves the structural efficiency of generated reasoning, and reallocates reasoning effort away from redundant verification and backtracking toward more productive exploration.