I want to submit some code that generated by lex and bison. Since there are gnu marks in them, I'm serious if it will become a trouble later to a non open source, commercial project.
Thanks for any suggestion.
lex (you are probably referring to flex) is not a GNU project, and is not GPL-licensed (it uses the permissive BSD license instead). So there are no "gnu marks" in its output. You may be talking about text such as
#line 3 "lex.yy.c"
#define YY_INT_ALIGNED short int
/* A lexical scanner generated by flex */
#define FLEX_SCANNER
#define YY_FLEX_MAJOR_VERSION 2
#define YY_FLEX_MINOR_VERSION 5
#define YY_FLEX_SUBMINOR_VERSION 35
#if YY_FLEX_SUBMINOR_VERSION > 0
#define FLEX_BETA
#endif
which are conventional C-preprocessor lines, unrelated to licensing.
Bison's output is explicitly addressed in its licensing, and is not a problem:
The distribution terms for Bison-generated parsers permit using the parsers in nonfree programs.