AGADIR, Morocco, March 29, 2013 (AFP) - The 32-year-old, on 12-under at the halfway stage, is three shots ahead of Finland's Mikko Ilonen and England's David Horsey, the 2011 champion.
Siem needs to win the tournament to stand any chance of climbing into the world top 50 and earning a debut Masters appearance in Augusta next month.
On Friday, he carded seven birdies and three bogeys at Golf du Palais Royal.
"I am trying my best (to get to the Masters). It is a tournament I have always wanted to play and if I can keep calm and play the way that I have been for the first two days here then I have a chance," said the German.
"I hope the wind blows a little bit more because I enjoy the challenge of playing into the wind and it would also keep the guys behind me away from me because if there is no wind out there then people can go very low around this course."
Ilonen had seven birdies, an eagle, a bogey and a double bogey seven in an eventful 66 while Horsey carded 67.
Leading and selected second round scores in the European Tour Trophee Hassan II at Golf du Palais Royal on Friday (GBR/IRL unless stated; par 72):
132 - Marcel Siem (GER) 64-68
135 - Mikko Ilonen (FIN) 69-66, David Horsey 68-67
136 - Pablo Larrazabal (ESP) 72-64
138 - Craig Lee 69-69, Bernd Wiesberger (AUT) 72-66, Andreas Harto (DEN) 71-67
139 - Joost Luiten (NED) 70-69
140 - Garth Mulroy (RSA) 73-67, Chris Paisley 73-67, Simon Wakefield 68-72, Chris Lloyd 72-68
141 - Alvaro Velasco (ESP) 67-74, David Howell 71-70, Richard McEvoy 71-70, Gregory Havret (FRA) 70-71
142 - Mikael Lundberg (SWE) 73-69, Daniel Brooks 72-70, Scott Arnold (AUS) 71-71, Matthew Baldwin 72-70, Justin Walters (RSA) 71-71, Anthony Snobeck (FRA) 75-67, Oliver Fisher 73-69
143 - Richie Ramsay 74-69, Stephen Gallacher 75-68, Paul Waring 71-72, Scott Henry 72-71, Julien Quesne (FRA) 71-72, Jose Manuel Lara (ESP) 72-71, Michael Hoey 74-69
Selected:
144 - Daniel Popovic (AUS) 72-72
146 - Richard Green (AUS) 75-71, Keith Horne (RSA) 77-69
Missed cut:
148 - Brett Rumford (AUS) 73-75
149 - Daniel Gaunt (AUS) 75-74, Matthew Zions (AUS) 78-71, Kang Kyung-nam (KOR) 71-78, Jose-Maria Olazabal (ESP) 79-70
150 - Ewan Porter (AUS) 73-77
151 - Tjaart Van Der Walt (RSA) 78-73
159 - Carl Yuan (CHN) 84-75