Yes, you can do this with FrameworkElementFactory. Charles Petzold has a walkthrough in Chapter 11, Applications = Code + Markup, but the main idea is that you create a FrameworkElementFactory for the root element of the template (and other factories for any child elements), create a ControlTemplate, and set the VisualTree property of the ControlTemplate to FrameworkElementFactory:
FrameworkElementFactory borderFactory = new FrameworkElementFactory(typeof(Border));
// set properties and create children of borderFactory
ControlTemplate template = new ControlTemplate();
template.VisualTree = borderFactory;
myButtonInstance.Template = template;
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