All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
‘Aa’ishah narrated: “Whenever the Prophet went to bed every night, he used to cup his hands together and blow over them then recite Surat Al-Ikhlas [Quran 112], Surat Al-Falaq [Quran 113], and Surat An-Nas [Quran 114], and then rub his hands over whatever parts of his body he was able to rub, starting with his head, face, and front of his body. He used to do that three times.” [Al-Bukhari]
Ibn Hajar said in Fath al-Bari: “He used to do that when he went to bed, and he used to do it if he complained of anything in his body.” [End of quote]
Besides, Ibn Raslan said in Sharh Sunan Abu Dawood:
“‘And then rubs his hands over whatever parts of his body he was able to rub’; i.e., whatever his hands can reach from his entire body, so that this would be like a protection for him from evil matters at night, from pests and the like. He begins with his hands by wiping on his head because it is the best, most honorable, and highest part of the body, and on his face because it is the most honorable part of the head, then rubs whatever he can reach from the front side of his body as this comes in priority over the backside of his body, because what is on the right-hand side is better than what is in the left-hand side, and he used to do this three times.” [End of quote]
Based on the above, there is nothing wrong with you in wiping over your entire body with your hands after reciting Surat Al-Fatihah, Al-Ikhlas, and Al-Mu’awwidhatayn [Quran 113 and 114], whether when performing Ruqyah or when going to sleep for example.
Allah knows best.