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I have downloaded some files from census website and did some cleaning to get ZCTA map for new york, but I noticed that there are overlapped regions (some regions are inside others). For some statistical purposes, It needs to be isolated. I looked online for some answers but I couldn't find a convenient answer to this.

I ended up producing file similar to this one: http://catalog.opendata.city/dataset/nyc-zip-code-tabulation-areas/resource/eec14f19-9794-46ef-9bf4-7f6835ffbf4c

If search "Manhattan"; you will see these small squares inside big ones.

Can anyone who has experience with GIS explain why ? Is it problem related to drawing polygons or it's really overlapped.

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I've translated most of Census' Cartography files to GeoJSON and made them available here:

https://github.com/loganpowell/census-geojson

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