Extract by Mask Rasters don't line up with originals in ArcGis 9.3

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I have 3 features I'm trying to use to extract by mask a DEM raster layer. After I extract by mask the layers visually don't line up. when I try to do further analyses (.e.g, extract to point, slope, summary stats, etc.) it is clear that my mask does not line up with my features because I get -99999 as values in further analyses.

What went wrong? and what can I do to fix it?

I'll also note that my features were originally drawn polygons that I converted to features -- could this have anything to do with the problem?



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