To build UI from a UXML file, you must first load the file into a VisualTreeAsset, and then use the Instantiate() to instantiate without a parent, which creates a new TemplateContainer, or CloneTree(parent)) to clone inside a parent.
Once the UXML is instantiated, you can retrieve specific elements from the visual tree with UQuery.
The following example creates a custom Editor window and loads a UXML file as its content:
using UnityEditor;
using UnityEngine;
using UnityEngine.UIElements;
using UnityEditor.UIElements;
public class MyWindow : EditorWindow {
[MenuItem ("Window/My Window")]
public static void ShowWindow () {
EditorWindow w = EditorWindow.GetWindow(typeof(MyWindow));
VisualTreeAsset uiAsset = AssetDatabase.LoadAssetAtPath<VisualTreeAsset>("Assets/MyWindow.uxml");
VisualElement ui = uiAsset.Instantiate();
w.rootVisualElement.Add(ui);
}
}