How can I find two lines of the file, remove them, without reading the entire file ... ?

You don't!(*)

But with files that size it needn't take long at all. This removes the 3rd and 8 millionth lines in a 500MB/8 million line file in 10 seconds:

C:\test>dir 500MB.csv
31/07/2012  20:22       536,870,913 500MB.csv

C:\test>wc -l 500MB.csv
8388608 500MB.csv

[23:19:43.35] C:\test>perl -nle"$.==3 || $.==8e6 and next; print" 500M
+B.csv >nul
[23:19:53.65] C:\test>
[download]

(* If your file contains fixed length lines, then you can, but you still need to move most of the file to close up the gap at the beginning, so it doesn't gain you much.)