Another question I have come across: How do I select FDO Features inside a given boundary (polygon) using API?
Following C# code snippet demonstrates usage of MgFeatureQueryOptions.SetFilter() to select features inside a given boundary (polygon) :
//spatial relationship inside a basic filter
MgFeatureQueryOptions query = new MgFeatureQueryOptions();
query.SetFilter("Geometry INTERSECTS GeomFromText('POLYGON ((135450.170691914 176714.481673732, 136292.021019111 176121.027356537, 135961.299875354 175651.879698467, 135119.449548157 176245.334015662, 135450.170691914 176714.481673732))') ");
//Get the features
MgResourceIdentifier resId = new MgResourceIdentifier(fsId);
MgFeatureReader ftrRdr = fs.SelectFeatures(resId, className, query);
Hope this is useful to you!