Children left teddy bears outside a bungalow in Kirkaldy's Dunvegan Avenue.
Hundreds of floral tributes, cards, and flowers have been placed near the flat where Mikaeel lived, as well as at the Fife property where he was found.
Mikaeel's body was found in woodland behind the house where his aunt lives shortly before midnight on Friday.
The boy's mother Rosdeep Kular, 33, is due to appear in court today charged in connection with her son's death.
A major police investigation was launched to find the three-year-old after he was reported missing from his home in Edinburgh's Ferry Gait Crescent last Thursday. More than 200 members of the public joined police and other agencies in their searches for the youngster in the Drylaw area of the capital on Friday.
A police helicopter, sniffer dogs, coastguard and lifeboat teams were brought in to help search for the toddler.
Neighbours on the modern housing estate also joined the hunt for Mikaeel, combing areas near his home such as parks and lock-ups.
After the discovery of his remains, investigators cordoned off the bungalow in Dunvegan Avenue. Last night they were still examining it and a wooded area behind the property that was also sealed off.
It was reported that Rosdeep Kular and her five children lived at the house until 18 months ago.
Reports also suggested Mikaeel was last seen at his nursery in December.
Rosdeep Kular told police that she put her son to bed at her Edinburgh home at 9pm on Wednesday, but when she went to wake him at 7.15am the following day he was missing.
She said on the night he allegedly vanished he was sleeping alone in the bedroom he normally shared with twin sister Ashika.
Rosdeep Kular was detained by police on Friday night after Mikaeel's body was found in woods near his aunt's house, more than 30 miles from Edinburgh.
Ms Kular was arrested and charged on Saturday, although the nature of the charge was not immediately made clear.