Boro’s best move of the game came on 12 minutes when Luca Colville spun past his marker in midfield and passed forward to Cartman, who flicked the ball on for Jake Day to surge past a defender and shoot narrowly wide.
Atherton went ahead in the 16th minute when the referee judged that Joe Amado had been shoved in the back by Thornton, and Matty Gilliam sent Ryan Whitley the wrong way from the penalty spot.
A jinking run from Luca Colville on 27 minutes saw him race past three defenders before laying off to Jake Day, who shot straight at the keeper.
Then James Cadman sent over a cross into the box, but it was just too high for Day to reach.
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In Atherton attacks, Dylan Cogill, who had an excellent game, twice won crucial headers to clear the danger, while on the stroke of half-time Marcus Cusani fired a shot inches past the far post.
Boro began the second half strongly, with Will Thornton glancing a header wide from a Ryan Watson corner.
Then the on-form Kieran Glynn displayed pace and trickery to burst through the middle, beating three men before laying off to Ryan Watson, who blazed a shot wide.
It took until the 51st minute for Boro to force visiting keeper Luke Hutchinson into a save, when he tipped a stinging Maloney shot round the post, and soon after, Watson had an effort blocked by a defender.
Jake Day then fired wide after connecting with a long ball forward from Cogill.
Atherton defended well whilst also looking dangerous on the break, as Danny Lambert had a shot blocked by Maloney, then Bailey Gooda headed a dangerous cross clear.
Luca Colville jinked past a defender and tried a shot, which was palmed round the post by the diving Hutchinson, then James Cadman raced down the right flank and curled a shot inches wide of the post.
Another surging run by Cadman ended with Day heading his cross narrowly over, and substitute Brad Plant lifted a shot just over the bar, while Plant and fellow sub Ash Jackson both fired shots straight at the keeper.
Atherton created a late chance, but Niall Battersby’s shot was easily saved by Ryan Whitley.
Right at the death Boro were handed a great chance to salvage a point when keeper Whitley launched a long ball forward towards Jake Day in the area, and a defender clumsily barged him to the ground.
The referee pointed to the spot, but Ryan Watson blasted his kick against the outside of the left hand post with virtually the last kick of the game.
Scarborough: Whitley, Cadman, Cogill (Jackson 69), Maloney (Plant 69), Thornton, Gooda, Colville, Watson, Cartman, Day, Glynn.
Man of the match: Kieran Glynn.