import re

string = """
Male    Name=Tony;  
Female  Name=Alice.1; 
Female  Name=Alice.2;
Male    Name=Ben; 
Male    Name=Shankar; 
Male    Name=Bala; 
Female  Name=Nina; 
###
Female  Name=Alex.1; 
Female  Name=Alex.2;
Male    Name=James; 
Male    Name=Graham; 
Female  Name=Smith;  
###
Female  Name=Xing;
Female  Name=Flora;
Male    Name=Steve.1;
Male    Name=Steve.2; 
Female  Name=Zac;  
###
"""

hashrx = re.compile(r'^###$', re.MULTILINE)
namerx = re.compile(r'Name=\w+(\.\d+)?;')

new_string = '###'.join([namerx.sub(r"Name=Class_{}\1".format(idx + 1), part) 
				for idx,part in enumerate(hashrx.split(string))])
print(new_string)