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I created a model to loop through a feature class and wish to use the individual record to clip raster and save as individual raster databaset based on that record extent. Here is my model:

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However, I am not sure why I cannot check the "Use Input Feature for Clipping Geometry" box. Does anyone has any idea?

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I am using ArcGIS 10.2.1

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Your problem is a recurring one in ModelBuilder. You need to set a default value for Feature Class. Once you do that, all the bubbles should have color and you'll be able to select that box. The reason you can't select it is ModelBuilder doesn't see any input features for you to use. Even if the model, while running, would have that information, it doesn't have it at this moment and it won't let you use nothing as an extent.

If that doesn't fix things, try Extract by Mask. That'll get you your output rasters in the right shape without having to bother with using a tool that isn't working like it should.

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