The first thing to consider with this question – Is your ball on the green? If your ball is off the green and there are no preferred lies in place then you cannot lift and clean your ball without penalty.
If your ball was sitting on the fringe, no matter whether you marked it with the toe of your putter, a ball marker, a tee or similar, if you lifted it to clean it, you would have broken Rule 9.4b and would incur a one stroke penalty.
Let’s assume for the purposes of answering this question that your ball is on the green.
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You’ve played a putt up to within a foot or two of the hole, and you’re looking to tap it in and get out of the way of your playing partners.
You don’t have a ball marker to hand, so you pop the toe of your putter behind the ball and leave it there. You then pick the ball up, give it a quick clean and place it back down on its original spot before tapping in.
The answer to that is – No. You have done nothing against the Rules of Golf.
That Rule continues to say, though, that the spot of the ball must be marked before it’s lifted.
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Now Rule 14.2 is relevant. You must replace the ball on its original spot. You can’t put your putter to the back of the ball and then replace it to the side of the putter.
You must also replace it correctly, setting it down by hand and letting it go. You cannot roll it into place with your foot or similar. If you don’t replace it correctly, you incur a one stroke penalty.
Rules Quiz