I have a project which involving several mating parts and also shaft guided through bearings, my issue here is that I don't have much experience with tolerances and manufacturing processes and I cannot determine the perfect balance between cost and accuracy. I am using Aluminium 6061 for raw material. For example I have some guidance "shafts" which are "made" by removing a large material from the part, I made some research and I saw that a +- 0.025 mm is a typical tolerance for a decent CNC machine. My question is, could I go down with that value, in terms of cost or is already a tight tolerance ?
It's going to be an uphill battle from that point on. While you can get every part of the machine and the process to tighter tolerances, their errors may compound to the sort of tolerance of 0.025; you may manufacture relatively simple parts with lower error but whether you succeed or not is more up to luck than your efforts - whether the tolerances of the tool, the table drive, the head drives, the frame rigidity, the sliders rigidity, and the material itself add up and ruin the accuracy or cancel each other resulting in near-perfect workpiece.
One nasty property to consider is the internal stresses of the material, resulting from the manufacturing process. If you remove large parts of it, the stresses that were canceled out by say, two outer surfaces pulling with equal strength against the central bulk pushing, will result in the workpiece ending as soon as you unlatch it. I had worked with 7mm brass sheets, and upon removing most of material from one side, I't observe good 2cm of deflection on a 30cm bar.
Regardless, if you aim at sub-0.01mm accuracy in all domains you can control (tool shape, material alignment, table flatness and machine being level), and the machine is good quality, you can expect better than 0.03mm accuracy in the result. If you want better, you'll need to get into the "guts" of the process - drives of the head and table, bearings, vibration dampening etc.