Fluent will scale whatever dimensions you tell it to. As it's accurate to many more significant figures than CAD (especially with double precision) it's been a route in for micro scale modelling for years. Your problem is the range of scales in CAD: if you're not careful even with scaling the curve faceting will close up the channel.
At 5 microns you're also into a flow regime that CFD codes aren't designed for. Yes it will work, but the resolution required may give time steps that are too small to solve in a reasonable time frame. You also need to read up on how your liquids interact with the material surfaces at that scale: CFD models assume a bulk surface property.