Removing gas boiler and baseboard system

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We had an HVAC system installed. The ugly baseboard heating wall units are still in place. The gas boiler also heats our water, but we'd like to go ahead and replace that with a new water heater. We want to remove the baseboards (as that system would no longer be functioning after installing the water heater), but would like some advice on the best manner to do this. The water lines need to be capped off, but how do we flush water out, push pipes sticking out of floor out of the way, etc. safely and correctly? Any advice would be great.