Thanks for the help from everyone - below is the code that I got to receive my result. I used help(string.split) in order to get my data to appear in the correct columns after the replacement. Also, the key was making line a string, in order to do the replacement.
import csv
import string
input_file = open('DesktopData.csv', 'r')
output_file = open('fixformat.csv', 'w')
data = csv.reader(input_file)
writer = csv.writer(output_file,quoting=csv.QUOTE_ALL)# dialect='excel')
specials = '%'
for line in data:
line = str(line)
new_line = str.replace(line,specials,'')
writer.writerow(new_line.split(','))
input_file.close()
output_file.close()