Set of Unity editor classes that provide a template for programatically refactoring prefabs. As a trivial example, this version changes all colliders to be triggers. Customize it to your needs by changing the code in RefactorTemplate.Refactor() (i.e. the component type you are searching for and what is done those components).

RefactorTemplate.cs

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

public class RefactorTemplate : MonoBehaviour
{
	[MenuItem("Refactor/Refactor")]
	static void Refactor()
	{
		GameObject[] prefabs = RefactorUtilities.LoadAllPrefabsWithComponent(typeof(Collider));
		foreach(GameObject prefab in prefabs)
		{
			Collider[] colliders = prefab.GetComponentsInChildren<Collider>(true);
			foreach(Collider collider in colliders)
			{
				collider.isTrigger = true;
				EditorUtility.SetDirty(collider);
			}
		}
	}
}

RefactorUtilities.cs

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

public class RefactorUtilities
{
	public static System.IO.FileInfo[] GetFileInfosForAssetsWithExtension(string fileExtension)
	{
		if(fileExtension != null && fileExtension.Length > 0 && fileExtension.IndexOf(".") != 0)
		{
			fileExtension = "." + fileExtension;
		}
		
		string searchPattern = fileExtension != null ? "*" + fileExtension : "*";
		System.IO.DirectoryInfo directory = new System.IO.DirectoryInfo(Application.dataPath);
		
		return directory.GetFiles(searchPattern, System.IO.SearchOption.AllDirectories);
	}
	
	public static string[] GetAssetPaths(string fileExtension)
	{
		System.IO.FileInfo[] fileInfos = GetFileInfosForAssetsWithExtension(fileExtension);
		
		List<string> paths = new List<string>();
		foreach(System.IO.FileInfo fileInfo in fileInfos)
		{
			paths.Add(fileInfo.FullName.Replace(Application.dataPath, "Assets"));
		}
		
		return paths.ToArray();
	}

	public static T[] LoadAssets<T>(string extension) where T : class
	{
		string[] paths = GetAssetPaths("controller");

		List<T> assets = new List<T>();
		foreach(string path in paths)
		{
			T asset = UnityEditor.AssetDatabase.LoadAssetAtPath(path, typeof(T)) as T;
			assets.Add(asset);
		}

		return assets.ToArray();
	}
	
	public static GameObject[] LoadAllPrefabsWithComponent(System.Type componentType)
	{
		string[] paths = GetAssetPaths("prefab");
		
		List<GameObject> prefabs = new List<GameObject>();
		foreach(string path in paths)
		{
			GameObject go = UnityEditor.AssetDatabase.LoadAssetAtPath(path, typeof(GameObject)) as GameObject;
			if(go.GetComponentsInChildren(componentType, true).Length > 0)
			{
				prefabs.Add(go);
			}
		}
		
		return prefabs.ToArray();
	}
}