I am supposed to do a hefsek tahara, but I have just gone to a doctor that did a procedure which caused scratches in the area in a way that likely caused bleeding. The hefsek tahara did not come out clean. Can I assume that the blood found on the hefsek came from the scratch, and thus begin counting shiva nekiim?

It is true that external bleeding (not from the uterus) does not make her a nidda, even if found on a bedika. More so, if one knows that she has such a scratch, then any blood found on the bedika can be attributted to having come from the scratch, and also would not make her a nidda or mess up her shiva nekiim. However, in regards to the main bedikot, namely the hefsek tahara and (one) bedika of day 1 and 7 of the shiva nekiim, it is not enough to attribute all the blood to the scratch, rather she must actually get a clean bedika from any blood in order to prove that she has stopped seeing nidda blood from the uterus. Therefore, in your case, even though you know that you have a scratch, you still need to have the hefsek tahara and bedikot of day 1 and 7 clean from all blood.

It is advisable to got to a nurse who can perform these bedikot (hefsek tahara, one bedika on day 1 and 7) while skipping over the area of the scratch. That way, you will be able to achieve clean bedikot.

חוו”ד סי’ קצו ס”ק ג