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The 21 cm spectral line emission of atomic neutral hydrogen (HI) is one of the primary wavelengths observed in radio astronomy. However, the signal is intrinsically faint and the HI content of galaxies depends on the cosmic environment, requiring large survey volumes and survey depth to investigate the HI Universe. As the amount of data coming from these surveys continues to increase with technological improvements, so does the need for automatic techniques for identifying and characterising HI sources while considering the tradeoff between completeness and purity. This study aimed to find the optimal pipeline for finding and masking the most sources with the best mask quality and the fewest artefacts in 3D neutral hydrogen cubes. Various existing methods were explored in an attempt to create a pipeline to optimally identify and mask the sources in 3D neutral hydrogen 21 cm spectral line data cubes. Two traditional source-finding methods were tested, SoFiA and MTObjects, as well as a new supervised deep learning approach, in which a 3D convolutional neural network architecture, known as V-Net was used. These three source-finding methods were further improved by adding a classical machine learning classifier as a post-processing step to remove false positive detections. The pipelines were tested on HI data cubes from the Westerbork Synthesis Radio Telescope with additional inserted mock galaxies. SoFiA combined with a random forest classifier provided the best results, with the V-Net-random forest combination a close second. We suspect this is due to the fact that there are many more mock sources in the training set than real sources. There is, therefore, room to improve the quality of the V-Net network with better-labelled data such that it can potentially outperform SoFiA.