Is the following what you want? You're given a table of pairs {f,C2} and you want to end up a table of pairs {f,(2*Integrate[C2])^0.5} ? If so, the following should work:
(* Create an example table where there are pairs {f,C1} *)
a = 5/100;
U = 13200;
L = 100;
C1 = Exp[-a (2 \[Pi] f \[Xi])/U ] * Cos[(2 \[Pi] f \[Xi])/U]
C2 = Table[{f, C1}, {f, 0, 1000, 5}]
(* Take the table of pairs of {f,C1} and create a table of pairs \
{f,(2*Integrate[C1^0.5])^0.5} *)
C3 = Table[{C2[[i,
1]], (2 NIntegrate[C2[[i, 2]]^0.5, {\[Xi], 0, L}])^0.5}, {i,
Length[C2]}]
(When you say in your Notebook that the X's aren't right, is that because the X's (or rather your values for f) were integrated, too?)