I ended up doing something like this (copy pasted from different places, so it doesnt add up, but you should get the general idea).

List<DirectoryInfo> directoryInfos = new List<DirectoryInfo>(dirInfo.GetDirectories("*", SearchOption.TopDirectoryOnly));

List<FileInfo> fileInfos = new List<FileInfo>(directoryInfo.GetFiles(fileMask, SearchOption.TopDirectoryOnly));

UnityEngine.Object obj = AssetDatabase.LoadAssetAtPath(filePath.Remove(0, path), type);

MonoScript script = obj as MonoScript;
if (script)
{
     Type scriptType = script.GetClass();
     if (scriptType.IsSubclassOf(typeof(MonoBehaviour)))
     {
          UnityEngine.Object obj = UnityEngine.Object.FindObjectOfType(scriptType);
          MonoBehaviour mono = obj as MonoBehaviour;
     }
}