Soft gamma repeaters and anomalous X-ray pulsars are thought to be magnetars , neutron stars with strong magnetic fields of order \mathord { \sim } 10 ^ { 13 } – 10 ^ { 15 } \gauss . These objects emit intermittent bursts of hard X-rays and soft gamma rays . Quasiperiodic oscillations in the X-ray tails of giant flares imply the existence of neutron star oscillation modes which could emit gravitational waves powered by the magnetar ’ s magnetic energy reservoir . We describe a method to search for transient gravitational-wave signals associated with magnetar bursts with durations of 10s to 1000s of seconds . The sensitivity of this method is estimated by adding simulated waveforms to data from the sixth science run of Laser Interferometer Gravitational-wave Observatory ( LIGO ) . We find a search sensitivity in terms of the root sum square strain amplitude of h _ { \mathrm { rss } } = 1.3 \times 10 ^ { -21 } \mathrm { Hz } ^ { -1 / 2 } for a half sine-Gaussian waveform with a central frequency f _ { 0 } = \SI { 150 } { \Hz } and a characteristic time \tau = \SI { 400 } { \s } . This corresponds to a gravitational wave energy of E _ { \mathrm { GW } } = 4.3 \times 10 ^ { 46 } \mathrm { erg } , the same order of magnitude as the 2004 giant flare which had an estimated electromagnetic energy of E _ { \mathrm { EM } } = \mathord { \sim } 1.7 \times 10 ^ { 46 } ( d / \SI { 8.7 } { \mathrm { kpc } } ) ^ { 2 % } \mathrm { erg } , where d is the distance to SGR 1806-20 . We present an extrapolation of these results to Advanced LIGO , estimating a sensitivity to a gravitational wave energy of E _ { \mathrm { GW } } = 3.2 \times 10 ^ { 43 } \mathrm { erg } for a magnetar at a distance of \SI { 1.6 } { kpc } . These results suggest this search method can probe significantly below the energy budgets for magnetar burst emission mechanisms such as crust cracking and hydrodynamic deformation .