You have to first convert the input to int using int()
print "Please key in the first log file you would like to use: "
choice1=raw_input()
.
.
filename1=filenames[int(choice1)]
.
or you could convert the input straight to int
choice1 = int(raw_input())
filename1 = filenames[choice1]
You should also display the list of files with their corresponding index numbers so the user would know which to choose.
UPDATE
For error handling, you can try something like
while True:
choice1 = raw_input('Enter first file name index: ')
if choice1.strip() != '':
index1 = int(choice1)
if index1 >= 0 and index1 < len(filenames):
filename1 = filenames[index1]
break // this breaks the while loop when index is correct
and the same for choice2