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I'm trying to build a raster map showing different subsoil features for a further analysis in ModFlow. I wonder how I can build a raster which shows different subsoil features?

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What software do you intend to use to build this raster? If that's part of the question, at least (please) indicate what formats the "subsoil features" are available in and what format is needed for input to ModFlow. –  whuber Mar 26 '12 at 20:30
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You may consider to work with voxels, see for example http://grass.osgeo.org/wiki/Voxel and http://grass.osgeo.org/grass70/manuals/html70_user/raster3dintro.html

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