The way to exterminate these subtlest (vestigial) saṁskāras is similar to the way adopted by sādhaka to eliminate the obstacles in the path of yoga.
Vyāsa Maharṣi says in his Pātañjala Yogasūtra Bhāṣya:
यथा क्लेशा दग्ध बीजभावा न प्ररोहसमर्था भवन्ति, तथा ज्ञानाग्निना दग्ध बीजभावः पूर्वसंस्कारो न प्रत्ययप्रसूर्भवति। ज्ञानसंस्कारास्तु चित्ताधिकारसमाप्ति मनुशेरत इति न चिन्त्यन्ते॥
Meaning: The arduous pestering afflictions are like burnt seeds that do not sprout despite having favourable conditions. Similarly, the pūrvasaṁskāras (past impressions) that are burnt in discriminatory knowledge (true jñāna) do not impregnate the notions. These impressions of true jñāna dawn only when there is cittavr̥ttinirodha. Hence to destroy these impressions, no more additional tools are required.
Patañjali suggests a solution to eliminate latent saṁskāras here by hyperlinking this sūtra to sūtras 2.10 and 2.11. Read these once again:
2.10: Subtler and residual impressions of (five obstacles) can be wiped out by withdrawal of mind to its source (pratiprasava).
2.11: The subtler obstacles might breed subtler vṛttis — fluctuations of the mind and these can be completely and effectively annihilated by profound meditation.
But there should be a constant spiritual struggle on the part of sādhakas till ultimate wisdom is realized (Bhagavad Gītā 2.59) so that embryonic impressions are also annihilated. Bhagavān continues with psychic surgery as follows:
यततो ह्यपि कौन्तेय पुरुषस्य विपश्चितः।
इन्द्रियाणि प्रमाथीनि हरन्ति प्रसभं मनः॥गीता २.६०॥
तानि सर्वाणि संयम्य युक्त आसीत मत्परः।
वशे हि यस्येन्द्रियाणि तस्य प्रज्ञा प्रतिष्ठिता॥गीता २.६१॥
yatato hyapi kaunteya Puruṣasya vipaścitaḥ।
indriyāṇi pramāthīni haranti prasabhaṁ manaḥ॥Gītā 2.60॥
tāni sarvāṇi saṁyamya yukta āsīta matparaḥ।
vaśo hi yasyendriyāṇi tasya prajña pratiṣṭhitā॥Gītā 2.61॥
Though the sādhaka is steadfast in his efforts for spiritual upliftment, the senses could be so powerful that he could be swept away and shaken from his sādhana. The solution lies in controlling these bizarre senses and surrendering to Me. The astuteness or wisdom of such a person would be stable when the senses are under command.
When the senses are in command, Bhakti rises up in the bosom of a devotee like swelling of the sea on full moon day, or like rising of Sun in the east, or like blooming of a flower. A vibrant flowing river is so indifferent to what is thrown to it that everything would be swept away to the ocean without any kind of prejudice.
Bhagavān declares the supremacy of the Bhaktiyoga in this verse:
प्रलयं हे गमिष्यन्ति श्रीमद्भागवतध्वनेः।
कलेर्दोषा इमे सर्वे सिंहशब्दाद् वृका इव॥ भागवतपुराणम् २.६२॥
Pralayaṁ hi gamiṣyanti śrīmadbhāgavatadhvaneḥ|
Kalerdoṣā ime sarve siṁhaśabdād vṛkā iva॥Bhāgavatam 2.62॥
The very roar of a lion makes the wolves run away. So do the vices of Kaliyuga; they would just vanish with the very sound of Bhāgavatam, that is the Gospel of Bhaktiyoga, says Nārada Maharṣi