rather than using a cleaning syphon, use a turkey baster. the opening is wider so they won't get injured. just suck them up and squirt them into a container for transfer tothe otehr tank. thats how i separated my smaller fry. of course, once theyre a little bigger, they will be okay in the main tank and separating isn't necessary. what kind of fry are they? what else do you have in the tank? many will hide quite well in the gravel and still survive. or you could spend a few buck and get some fake plants geared towards fry (usually a short grassy like thing that sits onteh bottom of the tank). fake plants only cost a few dollars after all. i left a number of fry in my tank at first to see how they'd fair, and they actually grew faster and larger than the ones i separted.