MacDonald, who has netted 18 times this season, will miss the rest of the season with a shoulder injury and Scott expects Clarke, who joined from Ipswich last month, to give the Bees some sting in the last five matches of the campaign.
"We won't be seeing Charlie again this season which is a big disappointment, but we've got Billy who can take his chance to score goals," Scott told the Hounslow and Chiswick Guardian.
"He has got a bit of devilment about him. He's very passionate about his football and wants to do well. He has come in and settled in very nicely."
Clarke has one goal in two appearances since joining from the Tractor Boys.