optimal solution is vague statement but if you were mapping using bbmap.sh from BBMap suite then you get the following choices of how to treat multi-mapping reads.

ambiguous=best          (ambig) Set behavior on ambiguously-mapped reads (with
                        multiple top-scoring mapping locations).
                            best    (use the first best site)
                            toss    (consider unmapped)
                            random  (select one top-scoring site randomly)
                            all     (retain all top-scoring sites)

You can choose ambig=random to keep one of the top scoring hits.

If this is in reference to RNAseq datasets then using a program like salmon (LINK) will allow you to intelligently treat these multi-mapping reads to generate expression estimates.