Sachi- Indenting stays for tire or ring (or rotor too) clearance usually is NBD given some care and thought with minor expectations as the goal. But one can do some real "harm" too, hence the care and thought part. This topic has been discussed here and in other forums many times and I suspect there are gems of wisdom to be found if searched for.
Here's the dimpling tool I use most of the time I need dented stays.

Made with hand tools and files. I like the modular design approach for tooling as I often will find later I want a slightly different detail on the tool. In this case I wanted to change the shape of the indent.

So I made a second form and backing plate.

And here's the resulting indent shapes. Both on oval chain stays. The RH stay has the first, long and narrow form and the LH is from the second wider form.
Both times the amount of added clearance per stay indent was only a couple of MMs. The oval shape reduces the indent's actual effect, a round stay will show a greater amount of clearance added for the same indent depth. On the actual frame's stays I do a running judgement as to how deep I need to go balanced with how much stay cross section is lost. IMO having to indent so far to gain more than a couple of Mms per side is suggesting you have the wrong bike/set up. Andy