you need to use two loop for as nested loop and than replace it
stopWords[] = {"and","the","etc"};
checkIN[]= {"religion","america","and","country","the"};
for(int i=0; i<=stopWords.Length; i++)
{
for(int j=0; i<=checkIN.Length; j++)
{
if(checkIN[j].ToString().IndexOf(stopWords[i].ToString() > 0)
{
//here found that content of stopword array in checkIN array so you need to replace with another text //what you want as follows
checkIN[j] = "new text here";
}
}
}