Changing substrate with fry in tank

I'm wondering if anyone could help me out a little. I want to change the substrate in my tank..which isn't a big deal to me, I can do it no problem. But my issue is that I have a few fry living among the rocks in my tank, and I don't know how I should go about dealing with them. Or should I not even bother right now with changing the substrate and wait for the fry to grow, or be eaten....which unfortunately has happenend before.

Or does anyone have a good safe way of catching fry that are no bigger than 1/2"? One of my biggest concern is that I would be moving their rocks that they have been living in now for a while and have good hiding spots, and then introducing them to a new environment. I just don't want to lose my luck that I have so far, because these guys are the longest living fry in my tank to date.

Any suggestions would be great. Thanks