The ethanol content of fuel is fully dissolved, so the ethanol won’t be floating at the top. It is more likely that your problem is caused by water contamination, particularly if your vehicle has been standing for a long time. Ethanol is hygroscopic i.e. it absorbs moisture from the atmosphere. Over time, this ethanol/water mix then separates from the fuel and sinks to the bottom of the tank, where it lies harmlessly out of reach of the pick-up pipe until you go for a drive, whereupon it gets shaken up and disperses into droplets which are sucked into your fuel system, hence the rough running.
My advice would be to stand the vehicle on a level surface overnight, then drain about half a litre of fuel into a clear container and let it stand for a couple of minutes; if you can see one layer floating on top of another, then the bottom layer is water.
The rest of the fuel should now be OK; you might even notice an improvement in running, as the ethanol that has mixed with the water will also have been removed.