Pull out the stems at the root (as you should do all year after they flower) and they'll be fine. I know fk all about flowers, but my alstroemeria are doing great after about five years!
Not sure where you are in the country but I've never had a problem overwintering Alstromeria down south. They are generally considered hardy to -10 according to the RHS site Could wrap some fleece over them if frosts are forecast though.