Look up ManualResetEvent, as it is made to do specifically what you're asking for.
Your threads create a new reset event, and add it to an accessible queue that your main thread can use to see if any threads are still running.
// main thread owns this
private List<ManualResetEvent> _resetEvents;
...
// main thread does this to wait for executing threads to finish
WaitHandle.WaitAll(_resetEvents.ToArray(), 2000, false)
...
// worker threads do this to signal the thread is done
myResetEvent.Set();
I can give you more sample code if you want, but I basically just copied it from the couple articles I read when I had to do this a year ago or so.
Forgot to mention, you can't add this functionality to the default threads you'll get when your timer fires. So you should make your timer handler be very lean and do nothing more than prepare and start a new worker thread.
...
ThreadPool.QueueUserWorkItem(new WaitCallback(MyWorkerDelegate),
myCustomObjectThatContainsAResetEvent);