[Thinking and obsessive thoughts in prayer]

Answer (and Allah grants success): Thinking and obsessive thoughts are among the human traits upon which Allah created people; thus one cannot completely rid himself of this human nature. The worshiper must strive against obsessive thoughts and worldly preoccupations, and must focus on the meanings of the prayer—its remembrances and pillars. It has been reported: “A person has from his prayer only that of which his heart is present.”
Allah Most High praised those described thus: “Surely the believers have succeeded—those who are humble in their prayers.” [al-Muʾminūn:1–2] Consequently, a prayer into which obsessive thoughts and inner talk have entered is deficient, and its deficiency is according to the amount of obsessive thoughts that entered it.
The meaning of deficiency here is deficiency in reward: its reward is diminished in proportion to the extent of the obsessive thoughts—little or much. Such a prayer is not complete, yet it is a valid prayer if it fulfills the conditions, obligations, and pillars. By its validity we mean: it suffices the one who prayed it; he is not required to repeat it nor make it up; by performing it he has lifted the obligation and discharged the command—but he does not deserve from its reward except what corresponds to how present his heart was therein.
Know that presence of heart is indispensable at the entry into it; by that we mean the intention (niyyah).
Source : Min Thimār al-ʿIlm wa al-Ḥikmah vol.1