Im betting you arent using lexicals here. I think in all my time programming perl I've written something like @final =(); only a handful of times. Normally you dont need to clear arrays as scoping takes care of it for you. Without seeing more code its hard to say for sure but the code you have posted makes me think that your problem isn't really the one you think it is.

For instance if @final were lexically declared inside of a loop then taking a reference to it would be just fine as each pass through the loop the @final would actually be a different array.