Mumbai Police brought down the hoardings in a bid to prevent clashes between the Sena and the Bharatiya Janata Party (BJP), which are in a coalition government in Maharashtra but whose ties have worsened in recent times.
The hoardings came up on the eve of the Sena's annual Dussehra rally, and ahead of the first anniversary of the coalition government.
All the hoardings with a collage of pictures show Modi, when he was the Gujarat chief minister, bowing before the late Bal Thackeray.
[Will Shiv Sena pull out Maharashtra govt? 'No chance', says BJP]
A telling caption, critical of the BJP, mounted at various locations in the city and suburbs, read: "Have you forgotten those days? When all your arrogant heads used to fall at Balasaheb's feet?"
Other leaders shown either bowing before Thackeray or greeting him warmly include former prime minister Atal Bihari Vajpayee and BJP veterans LK Advani and Rajnath Singh.
Besides, the hoardings showed Thackeray with now President Pranab Mukherjee, NCP chief Sharad Pawar and MNS president Raj Thackeray, the incumbent Sena president Uddhav Thackeray's cousin.
The Sena's annual Dussehra rally, to be held at Shivaji Park on Thursday, is a major event in the party's political calendar.
The Sena has always prided itself as the 'Big Brother' vis-a-vis the BJP in Maharashtra, and led the first coalition government with the BJP as a junior ally in 1995-99.
But in recent times, particularly after the BJP formed a government in the state last year with the Sena as its junior ally, few BJP leaders and ministers go to the Thackeray household at Bandra - unlike in the past.
In contrast, BJP leaders including Modi and Arun Jaitley enjoy improved relations with NCP leader Pawar.
At regular intervals, the Sena has unleashed banners, posters or hoardings on the BJP, which in turn chooses to black out its ally from various events.
The Sena was kept out of three major infrastructure inaugurations by Modi last week.
On its part, a belligerent Sena forced the cancellation of Pakistani ghazal singer Ghulam Ali's concerts in Mumbai and Pune as well as talks between the Indian and Pakistani cricket boards.
Sena activists also smeared ink on the face of veteran journalist and former Advani aide Sudheendra Kulkarni at a book release function.