Microarray technology is a rapidly developing field and a powerful tool in genome and proteome analysis and drug screening. [1][2][3][4] Although several types of microarrays of oligonucleotides and peptides have been constructed, surface patterning methods are still a key challenge in the field of 'biochip' fabrication. Self-assembled monolayers (SAMs) of alkanethiols on gold surfaces are widely used in nanotechnology and serve as templates for the immobilization of biomolecules.[5] UV lithography is a well-established patterning scheme for SAMs [6][7][8] but less suitable for smaller series. Mechanical methods for patterning of SAMs have been developed and overcome this problem. Among them, microcontact printing [9] (lCP) and dip-pen nanolithography [10] are the most prominent ones. Although with lCP spatial resolutions better than 100 nm have been achieved, it is difficult to use lCP for multistep patterning procedures. Dip-pen nanolithography in turn is limited in speed. Attempts have been made to increase the speed of dip-pen methods by massive parallelization.[11]Electron-beam (e-beam) technology has attracted the interest of several groups, [12,13] and high-resolution structures were realized, but the equipment is very costly. Other techniques, such as X-ray lithography, [14] ink-jet printing [15,16] as well as nanografting, [17] and even near-field lithography, [18] were explored for this challenging task. Direct laser patterning of alkanethiols is a newer alternative patterning method. [19][20][21] We present a process, named submerged laser ablation (SLAB), which enables the preparation of complex patterned SAMs (Scheme 1), free gold areas suitable as electrodes, and in addition laser patterning of the substrate itself in a single process. With the SLAB process any contamination arising from metal particles formed during laser ablation is avoided. Monolayers made from a wide spectrum of molecules may be processed by this method. The only requirement of the molecules is that they carry a thiol group, which enables their reaction with gold. As the gold substrate layer may also be structured in the same process (at higher energies), the SLAB process may be useful in the preparation of various types of 'biochips'.A template-stripped gold (TSG) substrate, mounted onto a glass carrier by epoxy glue, is first covered with a SAM of a thiol (primary thiol). The assembly is then submerged into a solution of a second thiolated compound (secondary thiol or reactant). The laser beam incidents the TSG by passing through the reactant solution and the SAM formed by the first thiol. The area of gold surface where the laser beam hits is heated due to the partial absorption of the laser light. The intensity is chosen to be low enough not to cause any ablation process in the TSG layer itself but high enough to thermally split the sulfur-gold bond, which binds the primary thiol to the TSG substrate. The primary thiol is released from the surface in the direction of the laser beam movement. As soon as the laser beam proceeds...