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I have to split river channel polygon by fishnet in ArcGIS Desktop. There are 500 squares in fishnet of 1km sq area which overlay above river channel polygon.

Is there any tool in ArcGIS Desktop by which I can directly split the river channel polygon into 500 squares?

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If you have an Advanced level license then you could try the Split tool:

Splitting the Input Features creates a subset of multiple output feature classes.

The Split Field's unique values form the names of the output feature classes. These are saved in the target workspace.

You would use your polygon fishnet as the split feature class.

To get a text field to split on just add one and use the field calculate a value like "fc" concatenated with the object id as a string.

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Assuming you are interested in keeping both the fishnet and river polygon geometry and attributes in one feature class, you can use Union.

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