Trimming 3D data using shapefile

2015 7 24
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I have 3D global data; my objective is to extract this data for specific watershed. I can do it by specifying it by raw and column, but is there anyway one can remove the data outside the area of interest using the shape file of the basin. I mean just like we do it in ArcGIS using functions like Mask or Clip Management.
Thanks GA

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