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I have used the snapping tool to snap the vertex in 2 feature classes together where they contain slivers gaps and overlaps. This works fine however the tool executes this for the whole polygon and snaps vertex/edges and therefore can move lines where lines should not be moved and creates errors rather than fix the issue. How can I specify somehow to only snap those areas where the gaps and slivers are noticeable?

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    You need to select individual vertices when adjusting the polygon. Otherwise you are moving the whole shape. You can also look at topological editing. There are also tools in arcgis to remove slivers from polygons. – jbalk Nov 23 '17 at 6:28
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If I understand correctly, you have a series of polygons, which have slivers and overlaps and you would like to remove them?

One way to do this would be as follows:

  1. Create a larger polygon around the area where you want to remove the slivers and then use the "ERASE" tool in Arc / X-Tools / ET Geowizards to remove the original polygons from your larger AOI. This will leave you with some large polygons and smaller polygons where the slivers were between the original polygon features.
  2. I am not sure how your polygon layer looks (perhaps add a picture so we can see), but from a guess you can now easily see those areas in the erased polygon which were never slivers but rather are meant to be there. IE: those areas between polygons where data is in reality not there - these can be deleted through selecting areas larger than X. Where X is an area you can decide. Once these are deleted, you will be left with just the slivers.
  3. You can now use the "Eliminate" tool to merge the sliver polygons into the original polygon layer. If I recall you may need to start an edit session or have the sliver polygon layer selected, I can't quite recall.

Another tool to look at is the "Integrate" Tool - this tool reshapes the polygon to match the edges between the polygons - fixing the overlaps and slivers...I am not too familiar with this tool but it may help.

If you create a GDB and import your polygon layer into it, you can set up Topology Rules. These rules can be quite useful in identify those areas where you have issues with slivers and overlaps. It is a good way to check the final results of which ever method you use.

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