Yes. If PCR results in off-target amplification, it's best to optimize the reaction as much as possible. If PCR cannot be optimized, we recommend performing a gel extraction using the Monarch® Spin DNA Gel Extraction Kit (NEB #T1120). Up to 4 µl of purified DNA can be carried into a KLD reaction.
For help optimizing PCR, see these guidelines: https://www.neb.com/en-us/tools-and-resources/usage-guidelines/guidelines-for-pcr-optimization-with-thermophilic-dna-polymerases
