Вы можете использовать объект PageTemplateInfo:
PageTemplateInfo somepagetemplate = PageTemplateInfoProvider.GetPageTemplateInfo(DocumentContext.CurrentDocument.GetUsedPageTemplateId()); //where "SomeDocument" is a PageInfo object.
//Get page template zones
var zones = somepagetemplate.WebPartZones;
//Grab instance of templat
var instance = somepagetemplate.TemplateInstance;
//Find particular zone
var zone = zones.Find(a => a.ZoneID == "Test");
//Remove zone from template instance
instance.RemoveZone(zone);
//Update template object
somepagetemplate.Update();