Remove the inside stops, the molding trim on the side, top and bottom jambs that hold the window in place. Use a pry bar to lift the stop molding enough so the fastening nails can be pulled with the pry bar or a hammer. Work carefully to avoid cracking or breaking the molding, which will be re-installed when the new window is placed.
Take out the old window. Remove screws fastening its frame to the rough frame. Lift out the entire window if it is a single component with panes inside a fixed frame, of wood, vinyl or metal. Take it out in sections. Remove the top sash first, if it is that style. Leave the exterior stop, on the outer side of the window, in place. Clean the jambs on the sides, top and bottom of the window opening thoroughly to remove any debris or dirt.
Put a bead of caulk on the inside of the exterior stop. Set the replacement low-e window into the opening firmly against the exterior stop. Get it square and level. Use tapered wooden shims to adjust the new window frame as necessary until it is perfectly aligned in the opening. Secure it with mounting screws, which should come with the window, through holes in the finished frame into the rough frame.
Check the sashes to ensure they open properly if it is a double-sash window that can be raised; some windows have sashes that lift, others have segments that tilt our and some low-e styles cannot be opened. Re-install the interior stop at the side, top and bottom jambs. Use the original nail holes if possible. Attach the stop with finishing nails, set the heads and fill the holes with wood filler.