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Using a Definition Query for a layer is ignored by Spatial Analyst functions.
After setting up a query, running a Spatial Analyst function, such as Convert Features to Raster, all features, including those not displayed, are converted to raster.
This is a known issue with ArcGIS 8.1.
This problem has been resolved in ArcGIS 8.1.2.
In ArcGIS 8.1, you can use Select By Attributes to get around this problem.