When you convert an illustrator file or vector layer to a shape layer through "Create Shapes from Vector Layer", it might produce some annoying boxes around each shape. Recognisable by the combination of a "Group 1" directly followed by a "Merge Paths 1" property. Cleanup Shapes removes those annoying and superfluous (clipping box) properties from shape layers. Just select the desiderd shape layer(s) and press the "Cleanup Shape Layers" button from the panel. Watch the tutorial for more details. Place this script in the "ScriptUI Panels" folder within your After Effects applications scripts folder, for example in:

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The script can be downloaded here for free.