To uncover the relationship between neural activity and behavior, it is essential to reconstruct neural circuits. However, methods typically used for neuron reconstruction from volumetric electron microscopy (EM) dataset are often time-consuming and require extensive manual proofreading, making it difficult to reproduce in a typical laboratory setting. To address this challenge, we have developed a set of acceleration techniques that build upon the Flood Filling Network (FFN), significantly reducing the time required for this task. These techniques can be easily adapted to other similar datasets and laboratory settings. To validate our approach, we tested our pipeline on a dataset of Drosophila larval brain serial section EM images at synaptic-resolution level. Our results demonstrate that our pipeline significantly reduces the inference time compared to the FFN baseline method and greatly reduces the time required for reconstructing the 3D morphology of neurons.