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What tool can I use to run many shapefiles to intersect with a shapefile as a output?

It looks like that Iterate tools is use for feature classes or datasets and I don't see any for the shapefile.

I can use the Batch but I want to use ModelBuilder because I might need to add more tools later.

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A shapefile is a kind of feature class, like an FGDB feature class or an SDE feature class. Use iterate feature classes in modelbuilder. You can then output as a feature class, and if it is named correctly (c:\path\to\directory\that\exists\output.shp) you will get a shapefile out.

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