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I can intersect 2 layers with polygons using ArcMap. However I can specify only overall tolerance no matter what layer a feature is in (even same layer). So I either end up with lots of slivers if I don't tolerate snapping, or I end up collapsing small features from the first layer that I'd want to keep.

The problem is that I would like for features let's say less than 10 m apart in the first layer to stay as they are if they happen to be contained within some polygon of the second layer. However I'd like for edges of polygons of the 2nd layer to snap to those in the first layer if they are within 10 m.

I'm open to a solution using any tool be it ArcMap or some python library/script.

Here is the rough idea of what I want.

enter image description here

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Can you add some screenshots/drawings to try to explain your situation visually? –  blah238 Feb 18 '13 at 0:41
Are you already using geodatabase topology rules at all? Can you post a sample dataset? If you need a file host, see this meta thread for hosting suggestions. –  blah238 Feb 18 '13 at 1:15
Which version of ArcGIS are you using? –  blah238 Feb 18 '13 at 1:19
I'm using 9.3.1 with ArcInfo license. Yeah... I guess I missed that part on cluster tolerance. As for the data, I'd have to crop & strip it. I feel like topology rules is all I need... –  mlt Feb 18 '13 at 1:24
If you do find some rules that work I would encourage you to post your solution as an answer. It definitely sounds like a tricky problem! –  blah238 Feb 18 '13 at 1:32
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1 Answer

First run Integrate on both layers with your desired cluster tolerance and ranks.

After this just run the union tool.

Important usage tip (from ESRI help): Integrate permanently changes the input features. Integrate does not create new data, but, instead, modifies the original input features.

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I saw Integrate previously. It looks like it can adjust vertices only. Perhaps I should have given a better visual example. I'll update the question. I feel like there is no silver bullet. I feel like I'd have to use Spatial Adjustment with Edge Snapping and then Intersect followed by Eliminate tool. For Eliminate I'd have to figure out what I can call as a sliver I guess something based on area over square perimeter ratio. –  mlt Feb 19 '13 at 19:44
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