Gravitational waves emitted from compact binary coalescence can be subject to wave diffraction if they are gravitationally lensed by an intervening mass clump whose Schwarzschild time scale matches the wave period. Waves in the ground-based frequency band f∼10-103 Hz are sensitive to clumps with masses ME∼102-103 M enclosed within the impact parameter. These can be the central parts of low mass ML∼103-106 M dark matter halos, which are predicted in cold dark matter scenarios but are challenging to observe. Neglecting finely-tuned impact parameters, we focus on lenses aligned generally on the Einstein scale for which multiple lensed images may not form in the case of an extended lens. In this case, diffraction induces amplitude and phase modulations whose sizes ∼10%-20% are small enough so that standard matched filtering with unlensed waveforms do not degrade, but are still detectable for events with high signal-to-noise ratio. We develop and test an agnostic detection method based on dynamic programming, which does not require a detailed model of the lensed waveforms. For pseudo-Jaffe lenses aligned up to the Einstein radius, we demonstrate that a pair of fully upgraded aLIGO/Virgo detectors can extract diffraction imprints from binary black hole mergers out to zs∼0.2-0.3. The prospect will improve dramatically for a third-generation detector for which binary black hole mergers out to zs∼2-4 will all become valuable sources.