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To improve exclusion systems for fruit trees, insect nets of various types were evaluated for their permeability to different beneficial and pest species, under laboratory and field conditions. Pests studied were the apple maggot, Rhagoletis pomonella (Diptera: Tephritidae) and the spotted wing drosophila, Drosophila suzukii (Diptera: Drosophilidae). Beneficials were Aphidoletes aphidimyza (Diptera: Cecidomyiidae), Aphidius matricariae (Hymenoptera: Braconidae) and Aphelinus abdominalis (Hymenoptera: Aphelinidae). Mesh nets with five different apertures (square, rectangle, triangle, rhombus and hexagon) and six different sizes (from 0.4 to 2.8 mm) were 3D-printed from strands of polylactic acid and tested in the laboratory along with two commercially available nets made of polyethylene. The physical and behavioral characteristics of the six studied species affected their ability to cross the nets. For an equal size (open area), the intrusion rate was generally greater through the square- and/or hexagonal-shaped meshes. Rectangular-shaped apertures totally excluded the apple maggot in both laboratory and field trials, provided their shortest side did not exceed 1.9 mm. For the spotted wing drosophila, a maximum of 1.0 mm was similarly required for exclusion in the laboratory. The shape factor (length/width ratio) of the apertures appeared to affect net selectivity. Field trials confirmed that more aphid predators and leafroller parasitoids colonized trees covered with larger mesh nets (2.3 × 3.4 mm), while still excluding the apple maggot. Thus, for a similar aperture size (area), an elongated rectangular-shaped mesh appears to facilitate access for beneficials, while continuing to provide effective protection against apple pests.