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I have a shapefile of lakes with lots of polygons. The features I am interested in are only big lakes.

Is there any way to subset only the polygons I am interested in from the shapefile using ArcMap?

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You can use the Select (Analysis) tool which:

Extracts features from an input feature class or input feature layer, typically using a select or Structured Query Language (SQL) expression and stores them in an output feature class.

For your SQL expression use something like "Shape_Area" >= 10000 (or whatever threshold value you want to use)

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