It would be good if you could identify the type of flies because you could then target them more specifically. If it's blue bottles then I'd look for their food source & remove it. If it's small aphid types then you'd have to spray the tree's foliage or use a biological control available from gardeners suppliers. If it's mosquitoes then you can interupt the breeding cycle by removing all standing water. You can get fly killer in a felt tip marker style pen. It doesn't leave a visable mark! Just draw around the edge of the glass in your windows, around the bin, etc. For fly free ventilation you may have to install fly screens. Sticky velcro & tulle, or a staple gun & old net curtains will do the job if proper frames seem too much. Hope this helps.