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I have a large set of contours that I received broken down into several different subsets. I have merged most of the subsets together creating a larger set of contours in three different files. I have then created three different raster datasets from the contour shapefiles, however in that process, the rasters have a lot of zero elevation areas that shouldnt be there.

How do I get rid of these zero elevation areas to make a more accurate digital elevation model?

I was hoping the topo to raster tool would interpolate in between the different contours to clean up those areas but it did not. But, some of the zero elevation areas are in places where there is a stream, pond, or reservoir.

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You've started in the right place, TopoToRaster will do what you've asked (create a seamless elevation model from contours). There are a lot of options and it can be a bear to get right, as the length of the overview implies. I found it helpful to read the documents for the source tool, ANUDEM, so I could understand more of the theory.

Before that though, I'd start by

  • picking a small area that has a representative sample of the all the terrain types in your region -- hills, valleys, streams, waterbodies -- and
  • run T2R with a coarse cell size and fiddle with the options until you start getting what you're looking for. Pick a cell size large enough that it takes no more than a minute or two to return results. This will let you rapidly cycle through the options and narrow in what isn't working.
  • Add only one data layer at a time, start with contours only, and then add streams, waterbodies, etc. Make sure you select the right [field] and [type] for each feature class (field is "which attribute holds the elevation value?").
  • After doing a few runs of this go back to the docs, and they'll start to make more sense.
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first you create tin from contours

then you convert tin to raster/dem

here clip for you https://www.youtube.com/watch?v=MYAS2Bm-kZQ

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    Welcome to GIS SE. It would be good practice to include what tools and where to find them in your answer so that others with a similar problem can follow your answer. It is also good explain your video clip hyperlink as theey can get removed or changed. – Knightshound Dec 6 '16 at 10:18

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