There are a number of ways to exclude data from the analysis. Here are some;
1) from the Geostats help. "For data formats that support Null values, such as file and personal geodatabase feature classes, a Null value will be used to indicate that a prediction could not be made for that location or that the value showed be ignored when used as input. For data formats that do not support Null values, such as shapefiles, the value of -1.7976931348623158e+308 is used (this is the negative of the C++ defined constant DBL_MAX) to indicate that a prediction could not be made for that location."
2) or use the Make Feature Layer geoprocessing tool
3) or use the Select Layer By Attribute geoprocessing tool
-Steve