The whole of atk1.0-2.4.0 is listed under GNU-GPLv2.0. Can I take certain files out of GNU GPL license code and use it under different license / no license, or is this considered as obfuscation of GNU GPL licensed code?
Insofar as the GNU GPL license allows modification, you may modify a GPL-licensed work to no longer include certain files while retaining other files. However, you may only perform such distribution under the license terms granted by the work's copyright holder(s) -- typically the author(s) -- so you may not offer such a modified form under any terms other than the GPL (unless the copyright holder granted a different license option, either generally or privately to you specifically).
This is certainly not "obfuscation" of the GPL-licensed code, but if you use those files in binary form, you must also offer the corresponding source necessary to rebuild those binaries. Indeed, even if it did constitute obfuscation, outright obfuscation is not even automatically problematic, as long as you also distribute (or offer) a corresponding unobfuscated source form that is the "preferred form for making modifications" from which the obfuscated form was created. As a pratical example, you may offer a minified version of a GPL-licensed web application that loads faster over a network (at the cost of readability and comprehensibility) as long as you also offer the readable unminified version under the GPL to all recipients of the minified code.
If you include those files in a new work with other files, then the entire work may be distributed only if you distribute it as a whole under the GPL. This obligation to license other material under the GPL extends as far as copyright law understands the upstream GPL-licensed work to exist in the same copyrightable work as that other material.