Generation of focused multiple ion beamlets from an intense microwave plasma source is investigated for the creation of localized subsurface modification of materials. Unlike conventional single element focused ion beam (FIB) systems, the plasma source is capable of providing ion beams of multiple elements. Two types of plasma electrodes (PE) are employed, one with a honeycomb structure with notched apertures and another with a 5×5 array of through apertures, both attached to the plasma source and are capable of generating focused ion beamlets (50 - 100 μm diameter) in a patterned manner. Measurements of ion saturation current near the PE indicate that the plasma is uniform over an area of ∼ 7 cm2, which is further confirmed by uniformity in extracted beam current through the apertures. The ion beams are applied to investigate change in electrical sheet resistance Rs of metallic thin films in a controlled manner by varying the ionic species and beam energy. Results indicate a remarkable increase in Rs with beam energy (∼ 50 % at 1 keV for Ar ions), and with ionic species (∼ 90% for Krypton ions at 0.6 keV), when 80 nm thick copper films are irradiated by ∼2 cm diameter ion beams. Ion induced surface roughness is considered as the main mechanism for this change as confirmed by atomic force microscopy (AFM) measurements. Predictions for micro-beamlet induced change in Rs are discussed. The experimental results are verified using TRIM and AXCEL-INP simulations