Yes, a Recife was recently published in APL by belova and Dahlberg .  I believe IT should be possible by Inkjet Pristina although not to the precision as is possible by three d Pristina using FiB system.

Maybe you can use Sato and Kobayashi's metal mask process [ http://dx.doi.org/10.1143/JJAP.36.L200 ].  It has been used to make magnetic tunnel junction (MTJ) having AlOx barrier and in-plane ferromagnetic layers [ http://purl.lib.ua.edu/2154 ].  It might be possible to apply it to perpendicular MTJ (pMTJ), but I don't remember seeing any reports of it being successfully used for pMTJ.

A semiconductor-based process is the standard process used to make pMTJ, which requires deposition equipment (usually a sputter system), etching equipment (usually an ion beam etching system also known as an ion milling system), lithography equipment (at least photolithography, but e-beam lithography is usually used too), and annealing equipment (usually a magnetic vacuum annealer [e.g., http://micromagnetics.com/products_spintherm.html ]; though, it looks like someone else was able to do it with a heat gun [ http://dx.doi.org/10.1063/1.2837618 ]). There is a stepwise planarization process that has been successfully used to make pMTJ at a university [ http://mint.ua.edu/wp-content/uploads/2010/07/fall2009_18.pdf , http://purl.lib.ua.edu/13880 , http://purl.lib.ua.edu/77737 ].

A five layer stack on top of a substrate might be the simplest for you to start with.  For example, a thermally oxidized silicon substrate, a bottom Ta seed and electrode layer, a CoFeB fixed layer, a MgO barrier layer, a CoFeB free layer, and Ta capping and electrode layer [ http://www.nature.com/articles/srep02883 , http://www.researchgate.net/publication/234946543_Annealing_effects_on_CoFeB-MgO_magnetic_tunnel_junctions_with_perpendicular_anisotropy ].

I couldn't find any references, but I think CoFeB can sometimes be challenging to work with due to oxidization, stoichiometry, or some other problem(s).  If you instead used a Pd or Pt-based multilayer[ https://www.researchgate.net/publication/257949214_Large_enhanced_perpendicular_magnetic_anisotropy_in_CoFeBMgO_system_with_the_typical_Ta_buffer_replaced_by_an_Hf_layer ], you should not have to worry about off-stoichiometry deposition, but using a multilayer may have its own challenges like the material (e.g., Pt) can be expensive to buy and interdiffusion between layers might be issues.

Article Annealing effects on CoFeB-MgO magnetic tunnel junctions wit...

Article Large enhanced perpendicular magnetic anisotropy in CoFeB/Mg...

My group has the following papers on PMA, that may be useful to you. High vacuum magnetic thermal annealing is very important in obtaining PMA. Also thickness control of the CoFeB layer is critical. Make sure its thickness is about 1 nm.

https://www.researchgate.net/publication/274073867_Giant_Spin_Hall_Effect_and_Switching_Induced_by_Spin-Transfer_Torque_in_a_WCo40Fe40B20MgO_Structure_with_Perpendicular_Magnetic_Anisotropy

https://www.researchgate.net/publication/275829961_Beta_%28%29_tungsten_thin_films_Structure_electron_transport_and_giant_spin_Hall_effect

https://www.researchgate.net/publication/278016772_Giant_spin_Hall_effect_and_magnetotransport_in_a_TaCoFeBMgO_layered_structure_A_temperature_dependence_study

https://www.researchgate.net/publication/234900073_Ferromagnetic_resonance_and_damping_properties_of_CoFeB_thin_films_as_free_layers_in_MgO-based_magnetic_tunnel_junctions

Article Giant Spin Hall Effect and Switching Induced by Spin-Transfe...

Article Beta (β) tungsten thin films: Structure, electron transport,...

Article Giant spin Hall effect and magnetotransport in a Ta/CoFeB/Mg...

Article Ferromagnetic resonance and damping properties of CoFeB thin...

Many thanks prof Gang Xiao