用到的相关API

AssetDatabase.FindAssets：获取目标路径下符合过滤器要求的所有资源的GUID（GUID是一个资源文件的唯一标识符）
AssetDatabase.GUIDToAssetPath：GUID转路径
PrefabUtility.LoadPrefabContents：载入给定路径的预制体
PrefabUtility.SaveAsPrefabAsset：保存预制体到指定路径
PrefabUtility.UnloadPrefabContents：释放通过LoadPrefabContents加载的预制体

示例代码

using UnityEditor;
using UnityEngine;
using System.Collections.Generic;

// 在编辑器中修改预制体
public class Fan_ModifyPrefabs 
{
    // 获取该目录下（包括其各子孙目录）的所有预制体
    private static string path = "Assets/Fan";

    [MenuItem("Fan/Add BoxCollider to Prefab")]
    private static void AddBoxColliderToPrefab()
    {
        // 获取目标目录下所有预制体
        Dictionary<string, GameObject> pathAndPrefabDict = new Dictionary<string, GameObject>();
        string[] guids = AssetDatabase.FindAssets("t:prefab", new[] {path});
        foreach (var guid in guids)
        {
            string path = AssetDatabase.GUIDToAssetPath(guid);
            pathAndPrefabDict[path] = PrefabUtility.LoadPrefabContents(path);
        }

        // 为其添加BoxCollider
        foreach (var path in pathAndPrefabDict.Keys)
        {
            GameObject prefab = pathAndPrefabDict[path];
            if (prefab.GetComponent<BoxCollider>() == null)
            {
                prefab.AddComponent<BoxCollider>();
                Debug.Log(string.Format("为{0}添加了碰撞体！", prefab.name));
                PrefabUtility.SaveAsPrefabAsset(prefab, path);
            }
            else
            {
                Debug.Log(string.Format("{0}已有碰撞体，无法添加！", prefab.name));
            }

            PrefabUtility.UnloadPrefabContents(prefab);
        }
    }
}