A near-infrared femtosecond laser is focused by a 100 mm-focal-length plano-convex lens to form a laser filament, which is employed to drill holes on copper targets. By shifting or rotating the focusing lens, additional aberration is imposed on the focused laser beam, and significant influence is produced on the aspect ratio and cross-sectional shape of the micro-holes. Experimental results show that when proper aberration is introduced, the copper plate with a thickness of 3 mm can be drilled through with an aspect ratio of 30, while no through-holes can be drilled on 3-mm-thickness copper plates by femtosecond laser with minimized aberration. In addition, when femtosecond laser filament with large astigmatism is used, micro-holes that had a length to width ratio up to 3.3 on the cross-section are obtained. Therefore, the method proposed here can be used to fabricate long oval holes with high aspect ratios.